請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88340
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 李宣書 | zh_TW |
dc.contributor.advisor | Hsuan-Shu Lee | en |
dc.contributor.author | 王睦惠 | zh_TW |
dc.contributor.author | Mu-Hui Wang | en |
dc.date.accessioned | 2023-08-09T16:37:26Z | - |
dc.date.available | 2023-11-09 | - |
dc.date.copyright | 2023-08-09 | - |
dc.date.issued | 2023 | - |
dc.date.submitted | 2023-07-25 | - |
dc.identifier.citation | 1. Dawn B, Bolli R. Adult bone marrow-derived cells: regenerative potential, plasticity, and tissue commitment. Basic Res Cardiol. 2005;100(6):494-503.
2. Iismaa SE, Kaidonis X, Nicks AM, Bogush N, Kikuchi K, Naqvi N, et al. Comparative regenerative mechanisms across different mammalian tissues. npj Regenerative Medicine. 2018;3(1):6. 3. Patten J, Wang K. Fibronectin in development and wound healing. Adv Drug Deliv Rev. 2021;170:353-68. 4. Wu MY, Hill CS. Tgf-beta superfamily signaling in embryonic development and homeostasis. Dev Cell. 2009;16(3):329-43. 5. Ramirez H, Patel SB, Pastar I. The Role of TGFβ Signaling in Wound Epithelialization. Adv Wound Care (New Rochelle). 2014;3(7):482-91. 6. Penn JW, Grobbelaar AO, Rolfe KJ. The role of the TGF-β family in wound healing, burns and scarring: a review. Int J Burns Trauma. 2012;2(1):18-28. 7. Clevers H. Wnt/beta-catenin signaling in development and disease. Cell. 2006;127(3):469-80. 8. Steinhart Z, Angers S. Wnt signaling in development and tissue homeostasis. Development. 2018;145(11). 9. Whyte JL, Smith AA, Helms JA. Wnt signaling and injury repair. Cold Spring Harb Perspect Biol. 2012;4(8):a008078. 10. Diller RB, Tabor AJ. The Role of the Extracellular Matrix (ECM) in Wound Healing: A Review. Biomimetics (Basel). 2022;7(3). 11. Walma DAC, Yamada KM. The extracellular matrix in development. Development. 2020;147(10). 12. Martin P. Wound healing--aiming for perfect skin regeneration. Science. 1997;276(5309):75-81. 13. Gurtner GC, Werner S, Barrandon Y, Longaker MT. Wound repair and regeneration. Nature. 2008;453(7193):314-21. 14. Raja, Sivamani K, Garcia MS, Isseroff RR. Wound re-epithelialization: modulating keratinocyte migration in wound healing. Front Biosci. 2007;12:2849-68. 15. Chuong CM, Randall VA, Widelitz RB, Wu P, Jiang TX. Physiological regeneration of skin appendages and implications for regenerative medicine. Physiology (Bethesda). 2012;27(2):61-72. 16. Wagner DE, Wang IE, Reddien PW. Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science. 2011;332(6031):811-6. 17. van Wolfswinkel JC, Wagner DE, Reddien PW. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment. Cell Stem Cell. 2014;15(3):326-39. 18. Wittlieb J, Khalturin K, Lohmann JU, Anton-Erxleben F, Bosch TC. Transgenic Hydra allow in vivo tracking of individual stem cells during morphogenesis. Proc Natl Acad Sci U S A. 2006;103(16):6208-11. 19. Hemmrich G, Khalturin K, Boehm AM, Puchert M, Anton-Erxleben F, Wittlieb J, et al. Molecular signatures of the three stem cell lineages in hydra and the emergence of stem cell function at the base of multicellularity. Mol Biol Evol. 2012;29(11):3267-80. 20. Major RJ, Poss KD. Zebrafish Heart Regeneration as a Model for Cardiac Tissue Repair. Drug Discov Today Dis Models. 2007;4(4):219-25. 21. Pfefferli C, Jaźwińska A. The art of fin regeneration in zebrafish. Regeneration (Oxf). 2015;2(2):72-83. 22. Sehring I, Mohammadi HF, Haffner-Luntzer M, Ignatius A, Huber-Lang M, Weidinger G. Zebrafish fin regeneration involves generic and regeneration-specific osteoblast injury responses. Elife. 2022;11. 23. Flowers GP, Sanor LD, Crews CM. Lineage tracing of genome-edited alleles reveals high fidelity axolotl limb regeneration. Elife. 2017;6. 24. Tu S, Johnson SL. Fate restriction in the growing and regenerating zebrafish fin. Dev Cell. 2011;20(5):725-32. 25. Hou Y, Lee HJ, Chen Y, Ge J, Osman FOI, McAdow AR, et al. Cellular diversity of the regenerating caudal fin. Sci Adv. 2020;6(33):eaba2084. 26. Poss KD, Wilson LG, Keating MT. Heart regeneration in zebrafish. Science. 2002;298(5601):2188-90. 27. Jopling C, Sleep E, Raya M, Martí M, Raya A, Belmonte JCI. Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation. Nature. 2010;464(7288):606-9. 28. Ebert AD, Diecke S, Chen IY, Wu JC. Reprogramming and transdifferentiation for cardiovascular development and regenerative medicine: where do we stand? EMBO Mol Med. 2015;7(9):1090-103. 29. Gargioli C, Slack JM. Cell lineage tracing during Xenopus tail regeneration. Development. 2004;131(11):2669-79. 30. Rodrigues AM, Christen B, Marti M, Izpisua Belmonte JC. Skeletal muscle regeneration in Xenopus tadpoles and zebrafish larvae. BMC Dev Biol. 2012;12:9. 31. Kragl M, Knapp D, Nacu E, Khattak S, Maden M, Epperlein HH, et al. Cells keep a memory of their tissue origin during axolotl limb regeneration. Nature. 2009;460(7251):60-5. 32. Sandoval-Guzman T, Wang H, Khattak S, Schuez M, Roensch K, Nacu E, et al. Fundamental differences in dedifferentiation and stem cell recruitment during skeletal muscle regeneration in two salamander species. Cell Stem Cell. 2014;14(2):174-87. 33. Wang H, Loof S, Borg P, Nader GA, Blau HM, Simon A. Turning terminally differentiated skeletal muscle cells into regenerative progenitors. Nat Commun. 2015;6:7916. 34. Porrello ER, Mahmoud AI, Simpson E, Hill JA, Richardson JA, Olson EN, et al. Transient regenerative potential of the neonatal mouse heart. Science. 2011;331(6020):1078-80. 35. Storer MA, Miller FD. Cellular and molecular mechanisms that regulate mammalian digit tip regeneration. Open Biol. 2020;10(9):200194. 36. Dolan CP, Imholt F, Yang TJ, Bokhari R, Gregory J, Yan M, et al. Mouse Digit Tip Regeneration Is Mechanical Load Dependent. J Bone Miner Res. 2022;37(2):312-22. 37. Yoon JH, Cho K, Garrett TJ, Finch P, Maden M. Comparative Proteomic Analysis in Scar-Free Skin Regeneration in Acomys cahirinus and Scarring Mus musculus. Sci Rep. 2020;10(1):166. 38. Maden M, Brant JO. Insights into the regeneration of skin from Acomys, the spiny mouse. Exp Dermatol. 2019;28(4):436-41. 39. Mastellos DC, Deangelis RA, Lambris JD. Inducing and characterizing liver regeneration in mice: Reliable models, essential "readouts" and critical perspectives. Curr Protoc Mouse Biol. 2013;3(3):141-70. 40. Pibiri M. Liver regeneration in aged mice: new insights. Aging (Albany N Y). 2018;10(8):1801-24. 41. Dekaney CM, Gulati AS, Garrison AP, Helmrath MA, Henning SJ. Regeneration of intestinal stem/progenitor cells following doxorubicin treatment of mice. Am J Physiol Gastrointest Liver Physiol. 2009;297(3):G461-70. 42. Slorach EM, Campbell FC, Dorin JR. A mouse model of intestinal stem cell function and regeneration. J Cell Sci. 1999;112 Pt 18:3029-38. 43. Shieh SJ, Cheng TC. Regeneration and repair of human digits and limbs: fact and fiction. Regeneration (Oxf). 2015;2(4):149-68. 44. Fernando WA, Leininger E, Simkin J, Li N, Malcom CA, Sathyamoorthi S, et al. Wound healing and blastema formation in regenerating digit tips of adult mice. Dev Biol. 2011;350(2):301-10. 45. McCusker C, Bryant SV, Gardiner DM. The axolotl limb blastema: cellular and molecular mechanisms driving blastema formation and limb regeneration in tetrapods. Regeneration (Oxf). 2015;2(2):54-71. 46. Min S, Whited JL. Limb blastema formation: How much do we know at a genetic and epigenetic level? J Biol Chem. 2023;299(2):102858. 47. Hay ED, Fischman DA. Origin of the blastema in regenerating limbs of the newt Triturus viridescens. An autoradiographic study using tritiated thymidine to follow cell proliferation and migration. Dev Biol. 1961;3:26-59. 48. Campbell LJ, Crews CM. Wound epidermis formation and function in urodele amphibian limb regeneration. Cell Mol Life Sci. 2008;65(1):73-9. 49. de Both NJ. The developmental potencies of the regeneration blastema of the axolotl limb. Wilhelm Roux Arch Entwickl Mech Org. 1970;165(3):242-76. 50. Muneoka K, Fox WF, Bryant SV. Cellular contribution from dermis and cartilage to the regenerating limb blastema in axolotls. Dev Biol. 1986;116(1):256-60. 51. Endo T, Bryant SV, Gardiner DM. A stepwise model system for limb regeneration. Dev Biol. 2004;270(1):135-45. 52. Satoh A, Gardiner DM, Bryant SV, Endo T. Nerve-induced ectopic limb blastemas in the Axolotl are equivalent to amputation-induced blastemas. Dev Biol. 2007;312(1):231-44. 53. Carlson JD, Maire JJ, Martenson ME, Heinricher MM. Sensitization of pain-modulating neurons in the rostral ventromedial medulla after peripheral nerve injury. J Neurosci. 2007;27(48):13222-31. 54. Kumar A, Godwin JW, Gates PB, Garza-Garcia AA, Brockes JP. Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate. Science. 2007;318(5851):772-7. 55. Makanae A, Mitogawa K, Satoh A. Co-operative Bmp- and Fgf-signaling inputs convert skin wound healing to limb formation in urodele amphibians. Dev Biol. 2014;396(1):57-66. 56. Singer M, Inoue S. The Nerve and the Epidermal Apical Cap in Regeneration of the Forelimb of Adult Triturus. J Exp Zool. 1964;155:105-16. 57. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, et al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet. 2009;41(12):1350-3. 58. Shi Y, Desponts C, Do JT, Hahm HS, Schöler HR, Ding S. Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell. 2008;3(5):568-74. 59. Huangfu D, Maehr R, Guo W, Eijkelenboom A, Snitow M, Chen AE, et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol. 2008;26(7):795-7. 60. Tweedell KS. The urodele limb regeneration blastema: the cell potential. ScientificWorldJournal. 2010;10:954-71. 61. Day RC, Beck CW. Transdifferentiation from cornea to lens in Xenopus laevis depends on BMP signalling and involves upregulation of Wnt signalling. BMC Dev Biol. 2011;11:54. 62. Pearl EJ, Barker D, Day RC, Beck CW. Identification of genes associated with regenerative success of Xenopus laevis hindlimbs. BMC Dev Biol. 2008;8:66. 63. Malloch EL, Perry KJ, Fukui L, Johnson VR, Wever J, Beck CW, et al. Gene expression profiles of lens regeneration and development in Xenopus laevis. Dev Dyn. 2009;238(9):2340-56. 64. Shaw T, Martin P. Epigenetic reprogramming during wound healing: loss of polycomb-mediated silencing may enable upregulation of repair genes. EMBO Rep. 2009;10(8):881-6. 65. Kretsovali A, Hadjimichael C, Charmpilas N. Histone deacetylase inhibitors in cell pluripotency, differentiation, and reprogramming. Stem Cells Int. 2012;2012:184154. 66. Tseng AS, Carneiro K, Lemire JM, Levin M. HDAC activity is required during Xenopus tail regeneration. PLoS One. 2011;6(10):e26382. 67. Mochii M, Taniguchi Y, Shikata I. Tail regeneration in the Xenopus tadpole. Dev Growth Differ. 2007;49(2):155-61. 68. Rouhana L, Tasaki J. Epigenetics and Shared Molecular Processes in the Regeneration of Complex Structures. Stem Cells Int. 2016;2016:6947395. 69. Tassava RA, Mescher AL. The roles of injury, nerves, and the wound epidermis during the initiation of amphibian limb regeneration. Differentiation. 1975;4(1):23-4. 70. Brockes JP, Kumar A. Comparative aspects of animal regeneration. Annu Rev Cell Dev Biol. 2008;24:525-49. 71. Singer M. Trophic functions of the neuron. VI. Other trophic systems. Neurotrophic control of limb regeneration in the newt. Ann N Y Acad Sci. 1974;228(0):308-22. 72. Boilly B, Albert P. In vitro control of blastema cell proliferation by extracts from epidermal cap and mesenchyme of regenerating limbs of axolotls. Rouxs Arch Dev Biol. 1990;198(8):443-7. 73. Singer M, Salpeter MM. The bodies of Eberth and associated structures in the skin of the frog tadpole. J Exp Zool. 1961;147:1-19. 74. Satoh A, Cummings GM, Bryant SV, Gardiner DM. Neurotrophic regulation of fibroblast dedifferentiation during limb skeletal regeneration in the axolotl (Ambystoma mexicanum). Dev Biol. 2010;337(2):444-57. 75. Singer M. The influence of the nerve in regeneration of the amphibian extremity. Q Rev Biol. 1952;27(2):169-200. 76. Goss RJ. Regenerative inhibition following limb amputation and immediate insertion into the body cavity. Anat Rec. 1956;126(1):15-27. 77. Mescher AL. Effects on adult newt limb regeneration of partial and complete skin flaps over the amputation surface. J Exp Zool. 1976;195(1):117-28. 78. Tassava RA, Garling DJ. Regenerative responses in larval axolotl limbs with skin grafts over the amputation surface. J Exp Zool. 1979;208(1):97-110. 79. Loyd RM, Tassava RA. DNA synthesis and mitosis in adult newt limbs following amputation and insertion into the body cavity. J Exp Zool. 1980;214(1):61-9. 80. Beck CW, Izpisua Belmonte JC, Christen B. Beyond early development: Xenopus as an emerging model for the study of regenerative mechanisms. Dev Dyn. 2009;238(6):1226-48. 81. Haberland M, Montgomery RL, Olson EN. The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet. 2009;10(1):32-42. 82. Bolden JE, Peart MJ, Johnstone RW. Anticancer activities of histone deacetylase inhibitors. Nat Rev Drug Discov. 2006;5(9):769-84. 83. Spallotta F, Tardivo S, Nanni S, Rosati JD, Straino S, Mai A, et al. Detrimental effect of class-selective histone deacetylase inhibitors during tissue regeneration following hindlimb ischemia. J Biol Chem. 2013;288(32):22915-29. 84. Hu E, Dul E, Sung CM, Chen Z, Kirkpatrick R, Zhang GF, et al. Identification of novel isoform-selective inhibitors within class I histone deacetylases. J Pharmacol Exp Ther. 2003;307(2):720-8. 85. Hess-Stumpp H, Bracker TU, Henderson D, Politz O. MS-275, a potent orally available inhibitor of histone deacetylases--the development of an anticancer agent. Int J Biochem Cell Biol. 2007;39(7-8):1388-405. 86. Hoxha E, Lambers E, Ramirez V. HDAC1 plays an important role in the differentiation of embryonic stem cells and induced pluripotent stem cells into cardiovascular lineages. Developmental Biology 2011;356(1):221-221. 87. Wu CH, Tsai MH, Ho CC, Chen CY, Lee HS. De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration. BMC Genomics. 2013;14:434. 88. Farkas JE, Freitas PD, Bryant DM, Whited JL, Monaghan JR. Neuregulin-1 signaling is essential for nerve-dependent axolotl limb regeneration. Development. 2016;143(15):2724-31. 89. Farkas JE, Monaghan JR. Housing and maintenance of Ambystoma mexicanum, the Mexican axolotl. Methods Mol Biol. 2015;1290:27-46. 90. Smith JJ, Putta S, Walker JA, Kump DK, Samuels AK, Monaghan JR, et al. Sal-Site: integrating new and existing ambystomatid salamander research and informational resources. BMC Genomics. 2005;6:181. 91. Iten LE, Bryant SV. Forelimb regeneration from different levels of amputation in the newt,Notophthalmus viridescens: Length, rate, and stages. Wilhelm Roux Arch Entwickl Mech Org. 1973;173(4):263-82. 92. Tank PW, Carlson BM, Connelly TG. A staging system for forelimb regeneration in the axolotl, Ambystoma mexicanum. J Morphol. 1976;150(1):117-28. 93. Yoshida M, Kijima M, Akita M, Beppu T. Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A. J Biol Chem. 1990;265(28):17174-9. 94. Stocum DL. The role of peripheral nerves in urodele limb regeneration. Eur J Neurosci. 2011;34(6):908-16. 95. Suzuki M, Satoh A, Ide H, Tamura K. Nerve-dependent and -independent events in blastema formation during Xenopus froglet limb regeneration. Dev Biol. 2005;286(1):361-75. 96. Gardiner DM, Muneoka K, Bryant SV. The migration of dermal cells during blastema formation in axolotls. Dev Biol. 1986;118(2):488-93. 97. Todd TJ. On the process of reproduction of the members of the aquatic salamander. Quarterly Journal of Science, Literature and the Arts. 1823;16, 84–96. 98. Glozak MA, Seto E. Histone deacetylases and cancer. Oncogene. 2007;26(37):5420-32. 99. Liu T, Kuljaca S, Tee A, Marshall GM. Histone deacetylase inhibitors: multifunctional anticancer agents. Cancer Treat Rev. 2006;32(3):157-65. 100. Wang G, Badylak SF, Heber-Katz E, Braunhut SJ, Gudas LJ. The effects of DNA methyltransferase inhibitors and histone deacetylase inhibitors on digit regeneration in mice. Regen Med. 2010;5(2):201-20. 101. Lv L, Sun Y, Han X, Xu CC, Tang YP, Dong Q. Valproic acid improves outcome after rodent spinal cord injury: potential roles of histone deacetylase inhibition. Brain Res. 2011;1396:60-8. 102. Taylor AJ, Beck CW. Histone deacetylases are required for amphibian tail and limb regeneration but not development. Mech Dev. 2012;129(9-12):208-18. 103. Chou CW, Wu MS, Huang WC, Chen CC. HDAC inhibition decreases the expression of EGFR in colorectal cancer cells. PLoS One. 2011;6(3):e18087. 104. Elder JT, Zhao X. Evidence for local control of gene expression in the epidermal differentiation complex. Exp Dermatol. 2002;11(5):406-12. 105. Markova NG, Karaman-Jurukovska N, Pinkas-Sarafova A, Marekov LN, Simon M. Inhibition of histone deacetylation promotes abnormal epidermal differentiation and specifically suppresses the expression of the late differentiation marker profilaggrin. J Invest Dermatol. 2007;127(5):1126-39. 106. Hughes MW, Jiang TX, Lin SJ, Leung Y, Kobielak K, Widelitz RB, et al. Disrupted ectodermal organ morphogenesis in mice with a conditional histone deacetylase 1, 2 deletion in the epidermis. J Invest Dermatol. 2014;134(1):24-32. 107. Tang J, Yan Y, Zhao TC, Gong R, Bayliss G, Yan H, et al. Class I HDAC activity is required for renal protection and regeneration after acute kidney injury. Am J Physiol Renal Physiol. 2014;307(3):F303-16. 108. Rosato RR, Almenara JA, Grant S. The histone deacetylase inhibitor MS-275 promotes differentiation or apoptosis in human leukemia cells through a process regulated by generation of reactive oxygen species and induction of p21CIP1/WAF1 1. Cancer Res. 2003;63(13):3637-45. 109. Chen S, Yao X, Li Y, Saifudeen Z, Bachvarov D, El-Dahr SS. Histone deacetylase 1 and 2 regulate Wnt and p53 pathways in the ureteric bud epithelium. Development. 2015;142(6):1180-92. 110. Kiffmeyer WR, Tomusk EV, Mescher AL. Axonal transport and release of transferrin in nerves of regenerating amphibian limbs. Dev Biol. 1991;147(2):392-402. 111. Mescher AL, Connell E, Hsu C, Patel C, Overton B. Transferrin is necessary and sufficient for the neural effect on growth in amphibian limb regeneration blastemas. Dev Growth Differ. 1997;39(6):677-84. 112. Satoh A, makanae A, Hirata A, Satou Y. Blastema induction in aneurogenic state and Prrx-1 regulation by MMPs and FGFs in Ambystoma mexicanum limb regeneration. Dev Biol. 2011;355(2):263-74. 113. Grunstein M. Histone acetylation in chromatin structure and transcription. Nature. 1997;389(6649):349-52. 114. Shahbazian MD, Grunstein M. Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem. 2007;76:75-100. 115. Ferris DR, Satoh A, Mandefro B, Cummings GM, Gardiner DM, Rugg EL. Ex vivo generation of a functional and regenerative wound epithelium from axolotl (Ambystoma mexicanum) skin. Dev Growth Differ. 2010;52(8):715-24. 116. Tanner K, Ferris DR, Lanzano L, Mandefro B, Mantulin WW, Gardiner DM, et al. Coherent movement of cell layers during wound healing by image correlation spectroscopy. Biophys J. 2009;97(7):2098-106. 117. Currie JD, Kawaguchi A, Traspas RM, Schuez M, Chara O, Tanaka EM. Live Imaging of Axolotl Digit Regeneration Reveals Spatiotemporal Choreography of Diverse Connective Tissue Progenitor Pools. Dev Cell. 2016;39(4):411-23. 118. McCusker CD, Diaz-Castillo C, Sosnik J, A QP, Gardiner DM. Cartilage and bone cells do not participate in skeletal regeneration in Ambystoma mexicanum limbs. Dev Biol. 2016;416(1):26-33. 119. Scheuing MR, Singer M. The effects of microquantitles of beryllium ion on the regenerating forelimb of the adult newt, Triturus. J Exp Zool. 1957;136(2):301-27. 120. Thornton CS. Influence of an eccentric epidermal cap on limb regeneration in Amblystoma larvae. Dev Biol. 1960;2:551-69. 121. Geraudie J, Ferretti P. Gene expression during amphibian limb regeneration. Int Rev Cytol. 1998;180:1-50. 122. Monaghan JR, Epp LG, Putta S, Page RB, Walker JA, Beachy CK, et al. Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration. BMC Biol. 2009;7:1. 123. Monaghan JR, Athippozhy A, Seifert AW, Putta S, Stromberg AJ, Maden M, et al. Gene expression patterns specific to the regenerating limb of the Mexican axolotl. Biol Open. 2012;1(10):937-48. 124. Knapp D, Schulz H, Rascon CA, Volkmer M, Scholz J, Nacu E, et al. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program. PLoS One. 2013;8(5):e61352. 125. Stewart R, Rascon CA, Tian S, Nie J, Barry C, Chu LF, et al. Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PLoS Comput Biol. 2013;9(3):e1002936. 126. Campbell LJ, Suarez-Castillo EC, Ortiz-Zuazaga H, Knapp D, Tanaka EM, Crews CM. Gene expression profile of the regeneration epithelium during axolotl limb regeneration. Dev Dyn. 2011;240(7):1826-40. 127. Diaz-Castillo C. Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells. PeerJ. 2017;5:e4004. 128. Paksa A, Rajagopal J. The epigenetic basis of cellular plasticity. Curr Opin Cell Biol. 2017;49:116-22. 129. Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, et al. The axolotl genome and the evolution of key tissue formation regulators. Nature. 2018;554(7690):50-5. 130. Hayashi S, Kawaguchi A, Uchiyama I, Kawasumi-Kita A, Kobayashi T, Nishide H, et al. Epigenetic modification maintains intrinsic limb-cell identity in Xenopus limb bud regeneration. Dev Biol. 2015;406(2):271-82. 131. Wang MH, Wu CH, Huang TY, Sung HW, Chiou LL, Lin SP, et al. Nerve-mediated expression of histone deacetylases regulates limb regeneration in axolotls. Dev Biol. 2019;449(2):122-31. 132. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10. 133. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics. 2005;21(16):3439-40. 134. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9. 135. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323. 136. McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40(10):4288-97. 137. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. 138. Futschik ME, Carlisle B. Noise-robust soft clustering of gene expression time-course data. J Bioinform Comput Biol. 2005;3(4):965-88. 139. Schwammle V, Jensen ON. A simple and fast method to determine the parameters for fuzzy c-means cluster analysis. Bioinformatics. 2010;26(22):2841-8. 140. Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284-7. 141. Gerber T, Murawala P, Knapp D, Masselink W, Schuez M, Hermann S, et al. Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration. Science. 2018;362(6413). 142. Leigh ND, Dunlap GS, Johnson K, Mariano R, Oshiro R, Wong AY, et al. Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution. Nat Commun. 2018;9(1):5153. 143. Ashley-Ross MA. The comparative myology of the thigh and crus in the salamanders Ambystoma tigrinum and Dicamptodon tenebrosus. J Morphol. 1992;211(2):147-63. 144. Rivera-Gonzalez GC, Morris SA. Tracing the Origins of Axolotl Limb Regeneration. Dev Cell. 2018;47(6):675-7. 145. Dunis DA, Namenwirth M. The role of grafted skin in the regeneration of x-irradiated axolotl limbs. Dev Biol. 1977;56(1):97-109. 146. Yokoyama H, Maruoka T, Ochi H, Aruga A, Ohgo S, Ogino H, et al. Different requirement for Wnt/beta-catenin signaling in limb regeneration of larval and adult Xenopus. PLoS One. 2011;6(7):e21721. 147. Wischin S, Castaneda-Patlan C, Robles-Flores M, Chimal-Monroy J. Chemical activation of Wnt/beta-catenin signalling inhibits innervation and causes skeletal tissue malformations during axolotl limb regeneration. Mech Dev. 2017;144(Pt B):182-90. 148. Vieira WA, Wells KM, Raymond MJ, De Souza L, Garcia E, McCusker CD. FGF, BMP, and RA signaling are sufficient for the induction of complete limb regeneration from non-regenerating wounds on Ambystoma mexicanum limbs. Dev Biol. 2019;451(2):146-57. 149. Makanae A, Hirata A, Honjo Y, Mitogawa K, Satoh A. Nerve independent limb induction in axolotls. Dev Biol. 2013;381(1):213-26. 150. Thornton CS. The effect of apical cap removal on limb regeneration in Amblystoma larvae. J Exp Zool. 1957;134(2):357-81. 151. Thornton CS. The inhibition of limb regeneration in urodele larvae by localized irradiation with ultraviolet light. J Exp Zool. 1958;137(1):153-79. 152. Satoh A, Bryant SV, Gardiner DM. Nerve signaling regulates basal keratinocyte proliferation in the blastema apical epithelial cap in the axolotl (Ambystoma mexicanum). Dev Biol. 2012;366(2):374-81. 153. Mescher AL, Neff AW. Regenerative capacity and the developing immune system. Adv Biochem Eng Biotechnol. 2005;93:39-66. 154. Nacu E, Glausch M, Le HQ, Damanik FF, Schuez M, Knapp D, et al. Connective tissue cells, but not muscle cells, are involved in establishing the proximo-distal outcome of limb regeneration in the axolotl. Development. 2013;140(3):513-8. 155. McCusker CD, Gardiner DM. Positional information is reprogrammed in blastema cells of the regenerating limb of the axolotl (Ambystoma mexicanum). PLoS One. 2013;8(9):e77064. 156. Godwin JW, Pinto AR, Rosenthal NA. Macrophages are required for adult salamander limb regeneration. Proc Natl Acad Sci U S A. 2013;110(23):9415-20. 157. Godwin JW, Debuque R, Salimova E, Rosenthal NA. Heart regeneration in the salamander relies on macrophage-mediated control of fibroblast activation and the extracellular landscape. NPJ Regen Med. 2017;2. 158. Fei JF, Schuez M, Knapp D, Taniguchi Y, Drechsel DN, Tanaka EM. Efficient gene knockin in axolotl and its use to test the role of satellite cells in limb regeneration. Proc Natl Acad Sci U S A. 2017;114(47):12501-6. 159. Voss SR, Palumbo A, Nagarajan R, Gardiner DM, Muneoka K, Stromberg AJ, et al. Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression. Regeneration (Oxf). 2015;2(3):120-36. 160. Erickson JR, Gearhart MD, Honson DD, Reid TA, Gardner MK, Moriarity BS, et al. A novel role for SALL4 during scar-free wound healing in axolotl. NPJ Regen Med. 2016;1:16016-. 161. Kragl M, Roensch K, Nusslein I, Tazaki A, Taniguchi Y, Tarui H, et al. Muscle and connective tissue progenitor populations show distinct Twist1 and Twist3 expression profiles during axolotl limb regeneration. Dev Biol. 2013;373(1):196-204. 162. Zeng L, Kempf H, Murtaugh LC, Sato ME, Lassar AB. Shh establishes an Nkx3.2/Sox9 autoregulatory loop that is maintained by BMP signals to induce somitic chondrogenesis. Genes Dev. 2002;16(15):1990-2005. 163. Rayman JB, Takahashi Y, Indjeian VB, Dannenberg JH, Catchpole S, Watson RJ, et al. E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. Genes Dev. 2002;16(8):933-47. 164. Liang J, Wan M, Zhang Y, Gu P, Xin H, Jung SY, et al. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol. 2008;10(6):731-9. 165. Shi YB. Unliganded thyroid hormone receptor regulates metamorphic timing via the recruitment of histone deacetylase complexes. Curr Top Dev Biol. 2013;105:275-97. 166. Dinsmore CE. Urodele limb and tail regeneration in early biological thought: an essay on scientific controversy and social change. Int J Dev Biol. 1996;40(4):621-7. 167. Tanaka EM. Regeneration: if they can do it, why can't we? Cell. 2003;113(5):559-62. 168. Wu CH, Huang TY, Chen BS, Chiou LL, Lee HS. Long-duration muscle dedifferentiation during limb regeneration in axolotls. PLoS One. 2015;10(2):e0116068. 169. Wu CH, Chen YJ, Wang MH, Chiou LL, Tseng WI, Lee HS. Diffusion tensor tractography reveals muscle reconnection during axolotl limb regeneration. PLoS One. 2017;12(3):e0173425. 170. Niwa H, Yamamura K, Miyazaki J. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene. 1991;108(2):193-9. 171. Okabe M, Ikawa M, Kominami K, Nakanishi T, Nishimune Y. 'Green mice' as a source of ubiquitous green cells. FEBS Lett. 1997;407(3):313-9. 172. Huang TY, Chang CC, Cheng NC, Wang MH, Chiou LL, Lee KL, et al. Re-epithelialization of large wound in paedomorphic and metamorphic axolotls. J Morphol. 2017;278(2):228-35. 173. Mansour N, Lahnsteiner F, Patzner RA. Collection of gametes from live axolotl, Ambystoma mexicanum, and standardization of in vitro fertilization. Theriogenology. 2011;75(2):354-61. 174. Casco-Robles MM, Yamada S, Miura T, Nakamura K, Haynes T, Maki N, et al. Expressing exogenous genes in newts by transgenesis. Nat Protoc. 2011;6(5):600-8. 175. Khattak S, Murawala P, Andreas H, Kappert V, Schuez M, Sandoval-Guzman T, et al. Optimized axolotl (Ambystoma mexicanum) husbandry, breeding, metamorphosis, transgenesis and tamoxifen-mediated recombination. Nat Protoc. 2014;9(3):529-40. 176. Schreckenberg GM, Jacobson AG. Normal stages of development of the axolotl. Ambystoma mexicanum. Dev Biol. 1975;42(2):391-400. 177. Diogo R, Murawala P, Tanaka EM. Is salamander hindlimb regeneration similar to that of the forelimb? Anatomical and morphogenetic analysis of hindlimb muscle regeneration in GFP-transgenic axolotls as a basis for regenerative and developmental studies. J Anat. 2014;224(4):459-68. 178. Maden M, Avila D, Roy M, Seifert AW. Tissue specific reactions to positional discontinuities in the regenerating axolotl limb. Regeneration (Oxf). 2015;2(3):137-47. 179. Butler EG. Regeneration of the urodele forelimb after reversal of its proximo-distal axis. J Morphol. 1955;96(2):265-81. | - |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88340 | - |
dc.description.abstract | 蠑螈以其在受傷後能夠重新生長大部分身體組織並恢復複雜結構的卓越能力而在脊椎動物中備受矚目。其中一個著名的例子就是牠們完全再生功能性肢體的能力。儘管在這個領域取得了重要進展,但對於控制肢體再生的分子信號的理解仍然有限。組蛋白去乙醯化酶(HDACs)在肢體再生過程中扮演著關鍵角色。本論文旨在研究HDAC1在蠑螈肢體再生中的參與情況。研究發現,在再生的早期分化階段之前,HDAC1表現呈雙相上調。使用MS-275等抑制HDAC活性的化合物會延遲幼體的肢體再生,而局部注射HDAC抑制劑則會阻礙HDAC活性、芽基組織的形成和隨後的肢體再生。HDAC1的表現在傷口表皮中更為明顯,且截肢前的去神經會阻止其表達上升和肢體再生。此外,補充神經因子有助於促進HDAC1的上調表達並增強肢體再生過程。這些發現顯示HDAC1在蠑螈肢體再生中的參與情況,並強調了神經因子在調節這一過程中的重要性。
此外,本研究探討了HDAC抑制對肢體再生轉錄反應的影響。轉錄組學分析揭示了表皮和軟組織中複雜的功能途徑。HDAC活性對阻止與組織發育和分化相關的基因過早表達至關重要。抑制HDAC1導致再生相關基因和WNT通路相關基因的過早活化。使用WNT抑制劑處理後,部分恢復HDAC1的抑制作用,改善芽基組織形成。 此外,本論文還建立紅色與綠色的轉基因蠑螈,並延續先前實驗室在肌肉接合方面的研究結果,旨在透過雙螢光移植的方式,觀察再生肢體的橫截面來檢測肌肉纖維的重新接合情況。結果顯示,不同肌肉之間的肌肉纖維接合速度不同,其中 gracilis 肌表現出外圍的重連特徵。此外,在遠端再生部位,RFP+的肌肉纖維對肌肉再生起到了貢獻作用,尤其是在小腿的腹肌表面。這個雙螢光嵌合體為瞭解蠑螈肢體再生的後期肌肉接合模式提供了新的視角。 本研究凸顯了HDAC1在蠑螈肢體再生中的重要作用。神經調控的HDAC1表達對於芽基組織的形成和成功再生至關重要。研究結果強調了在這一過程中涉及的基因表達模式和表觀遺傳修飾的複雜性。此外,肌肉纖維的重連動態為肢體再生的後期階段提供了深入的洞察。本論文推進了人們對於蠑螈肢體再生機制的理解。這些發現對於再生醫學研究具有重要意義,並可能對未來的治療方法做出貢獻。 | zh_TW |
dc.description.abstract | Axolotls are renowned for their remarkable ability to regenerate various body parts, including fully functional limbs, making them stand out among vertebrates. However, our understanding of the molecular mechanisms that govern limb regeneration in axolotls remains limited. Histone deacetylases (HDACs) have been identified as crucial players in this process. This thesis aimed to investigate the role of HDAC1 in axolotl limb regeneration. The study revealed a biphasic up-regulation of HDAC1 prior to the early differentiation stage of regeneration. Inhibition of HDAC activity using the compound MS-275 caused a delay in limb regeneration in larvae, while localized injection of HDAC inhibitors hindered HDAC activity, blastema formation, and subsequent limb regeneration. Notably, HDAC1 expression was more pronounced in the wound epidermis (WE), and denervation prior to amputation prevented its elevation and subsequent limb regeneration. Furthermore, supplementation of nerve factors promoted the up-regulation of HDAC1 expression and enhanced the process of limb regeneration. These findings shed light on the involvement of HDAC1 in axolotl limb regeneration and emphasize the significance of nerve factors in regulating this process.
Furthermore, this thesis delved into the transcriptional changes occurring during limb regeneration under HDAC inhibition. Transcriptome sequencing uncovered intricate functional pathways in both the epidermis and soft tissue (ST). The activity of HDACs was crucial in suppressing the premature expression of genes associated with tissue development and differentiation. Inhibiting HDAC1 resulted in premature activation of genes linked to regeneration and the WNT pathway. Interestingly, administering a WNT inhibitor partially reversed the effects of HDAC1 inhibition and enhanced blastema formation. In addition, this study established transgenic axolotls with red and green fluorescence, building upon previous research in muscle reconnection conducted in Dr. Lee’s laboratory. The aim was to observe the reconnection of muscle fibers in regenerative limbs through cross-sectional analysis using the double fluorescence transplantation method. The results revealed that the reconnection of muscle fibers varied in speed among different muscles, with the gracilis muscle exhibiting peripheral reconnection characteristics. Furthermore, in the distal regenerative regions, the RFP+ muscle fibers contributed to muscle regeneration, particularly on the ventral surface of the calf. This double fluorescence chimeric model provides a new perspective on the late-stage muscle reconnection patterns in axolotl limb regeneration. Overall, this thesis highlights the essential role of HDAC1 in axolotl limb regeneration. Nerve-mediated HDAC1 expression is crucial for blastema formation and successful regeneration. The findings underscore the intricate gene expression patterns and epigenetic modifications involved in the process. Furthermore, muscle fiber reconnection dynamics provide insights into the late stages of limb regeneration. In conclusion, this comprehensive study advances our understanding of the mechanisms underlying axolotl limb regeneration. The findings have implications for regenerative medicine research and may contribute to future therapeutic approaches. | en |
dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2023-08-09T16:37:26Z No. of bitstreams: 0 | en |
dc.description.provenance | Made available in DSpace on 2023-08-09T16:37:26Z (GMT). No. of bitstreams: 0 | en |
dc.description.tableofcontents | Contents
致謝 I 中文摘要 III Abstract V Contents VII List of Figures IX List of Tables XII List of Abbreviations XIII CHAPTER 1: Literature Review 1 1.1 Introduction 2 1.2 The Basic Cellular and Molecular Mechanisms of Tissue Repair and Regeneration 3 1.3 Model Organisms in Regeneration Research 4 1.4 Regeneration Process in Axolotl Limb Regeneration 11 1.5 Blastema Formation is a Unique Structure as a Sign for a successful limb regeneration 14 1.6 Hypothesis and Aims 15 Chapter 2: The Role of Nerve-Mediated HDAC Expression in the Regulation of Limb Regeneration in Axolotls Regulates Limb Regeneration in Axolotls 18 2.1 Summary 19 2.2 Introduction 20 2.3 Materials and Methods 22 2.4 Results 28 2.5 Discussion 34 2.6 Tables and Figures 38 Chapter 3: The Importance of Timing: Nerve-Mediated HDAC1 Regulates the Sequential Expression of Morphogenic Genes in Axolotl Limb Regeneration 52 3.1 Summary 53 3.2 Introduction 54 3.3 Materials and Methods 57 3.4 Results 62 3.5 Discussion 70 3.6 Tables and Figures 75 Chapter 4: Unraveling the Intricacies of Salamander Limb Regeneration: Insights into Muscle Fiber Reconnection 97 4.1 Summary 98 4.2 Introduction 99 4.3 Materials and Methods 101 4.4 Results 105 4.5 Discussion 109 4.6 Figures 114 Reference 127 List of Publications 140 | - |
dc.language.iso | en | - |
dc.title | 蠑螈肢體再生:神經介導表現之組蛋白去乙醯化酶之角色與雙螢光嵌合體肢體再生模式之建立 | zh_TW |
dc.title | Axolotl limb regeneration: The roles of nerve-mediated expression of histone deacetylases and establishment of a double fluorescence chimeric limb regeneration model | en |
dc.type | Thesis | - |
dc.date.schoolyear | 111-2 | - |
dc.description.degree | 博士 | - |
dc.contributor.coadvisor | 林劭品 | zh_TW |
dc.contributor.coadvisor | Shau-Ping Lin | en |
dc.contributor.oralexamcommittee | 林頌然;李士傑;張俊哲;宋麗英 | zh_TW |
dc.contributor.oralexamcommittee | Sung-Jan Lin;Shyh-Jye Lee;Chun-che Chang;Li-Ying Sung | en |
dc.subject.keyword | 蠑螈,肢體再生,組蛋白去乙醯化酶,神經因子,雙螢光嵌合體,肌肉接合, | zh_TW |
dc.subject.keyword | axolotl,limb regeneration,histone deacetylases (HDACs),nerve factors,double fluorescence chimeric,muscle fiber reconnection, | en |
dc.relation.page | 140 | - |
dc.identifier.doi | 10.6342/NTU202301772 | - |
dc.rights.note | 同意授權(全球公開) | - |
dc.date.accepted | 2023-07-27 | - |
dc.contributor.author-college | 生物資源暨農學院 | - |
dc.contributor.author-dept | 生物科技研究所 | - |
顯示於系所單位: | 生物科技研究所 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-111-2.pdf | 5.6 MB | Adobe PDF | 檢視/開啟 |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。