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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 丁照棣(Chau-Ti Ting) | |
dc.contributor.author | Chih-Kuan Chen | en |
dc.contributor.author | 陳志冠 | zh_TW |
dc.date.accessioned | 2021-05-13T06:48:39Z | - |
dc.date.available | 2019-02-16 | |
dc.date.available | 2021-05-13T06:48:39Z | - |
dc.date.copyright | 2017-02-16 | |
dc.date.issued | 2017 | |
dc.date.submitted | 2017-01-18 | |
dc.identifier.citation | Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ. 2004. Bmp4 and morphological variation of beaks in Darwin's finches. Science 305:1462-1465.
Adkins-Regan E. 2009. Hormones and sexual differentiation of avian social behavior. Dev Neurosci 31:342-350. Alev C, Shinmyozu K, McIntyre BA, Sheng G. 2009. Genomic organization of zebra finch alpha and beta globin genes and their expression in primitive and definitive blood in comparison with globins in chicken. Dev Genes Evol 219:353-360. Basu M, Mukhopadhyay S, Chatterjee U, Roy SS. 2014. FGF16 promotes invasive behavior of SKOV-3 ovarian cancer cells through activation of mitogen-activated protein kinase (MAPK) signaling pathway. J Biol Chem 289:1415-1428. Bhattacharjee MJ, Yu CP, Lin JJ, Ng CS, Wang TY, Lin HH, Li WH. 2016. Regulatory Divergence among Beta-Keratin Genes during Bird Evolution. Mol Biol Evol. Bicudo JEPW. 2010. Ecological and environmental physiology of birds. Oxford ; New York: Oxford University Press. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. Brown WRA, Hubbard SJ, Tickle C, Wilson SA. 2003. The chicken as a model for large-scale analysis of vertebrate gene function. Nature Reviews Genetics 4:87-98. Charvet CJ, Striedter GF. 2011. Developmental Modes and Developmental Mechanisms can Channel Brain Evolution. Front Neuroanat 5:4. Chen CF, Foley J, Tang PC, Li A, Jiang TX, Wu P, Widelitz RB, Chuong CM. 2015. Development, regeneration, and evolution of feathers. Annu Rev Anim Biosci 3:169-195. Chen CK, Ng CS, Wu SM, Chen JJ, Cheng PL, Wu P, Lu MJ, Chen DR, Chuong CM, Cheng HC, et al. 2016. Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken. Mol Biol Evol. Chuong C-M. 1998. Molecular basis of epithelial appendage morphogenesis. Austin, TX: R.G. Landes. Chuong CM, Widelitz RB, Ting-Berreth S, Jiang TX. 1996. Early events during avian skin appendage regeneration: dependence on epithelial-mesenchymal interaction and order of molecular reappearance. J Invest Dermatol 107:639-646. Clayton DF, Balakrishnan CN, London SE. 2009. Integrating genomes, brain and behavior in the study of songbirds. Curr Biol 19:R865-873. Clayton DF, George JM, Mello CV, Siepka SM. 2009. Conservation and expression of IQ-domain-containing calpacitin gene products (neuromodulin/GAP-43, neurogranin/RC3) in the adult and developing oscine song control system. Dev Neurobiol 69:124-140. Consortium ICGS. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716. Daly TJ, Buffenstein R. 1998. Skin morphology and its role in thermoregulation in mole-rats, Heterocephalus glaber and Cryptomys hottentotus. J Anat 193 ( Pt 4):495-502. Deeming DC, Reynolds SJ. 2015. Nests, eggs, and incubation : new ideas about avian reproduction. In. Dhouailly D. 2009. A new scenario for the evolutionary origin of hair, feather, and avian scales. J Anat 214:587-606. Dial KP, Jackson BE, Segre P. 2008. A fundamental avian wing-stroke provides a new perspective on the evolution of flight. Nature 451:985-989. Dunn JL, Alderfer JK, National Geographic Society (U.S.). 2011. National Geographic field guide to the birds of North America. Washington, D.C.: National Geographic Society. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194. Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP, Ferree S, George RD, Grogan T, et al. 2008. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26:317-325. Greenwold MJ, Sawyer RH. 2010. Genomic organization and molecular phylogenies of the beta (beta) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution. BMC Evol Biol 10:148. Hamburger V, Hamilton HL. 1992a. A Series of Normal Stages in the Development of the Chick-Embryo, (Reprinted from Journal of Morphology, Vol 88, 1951). Developmental Dynamics 195:231-&. Hamburger V, Hamilton HL. 1992b. A series of normal stages in the development of the chick embryo. 1951. Dev Dyn 195:231-272. Hornik C, Krishan K, Yusuf F, Scaal M, Brand-Saberi B. 2005. cDermo-1 misexpression induces dense dermis, feathers, and scales. Dev Biol 277:42-50. Hughes SH. 2004. The RCAS vector system. Folia Biologica 50:107-119. Jung HS, Francis-West PH, Widelitz RB, Jiang TX, Ting-Berreth S, Tickle C, Wolpert L, Chuong CM. 1998. Local inhibitory action of BMPs and their relationships with activators in feather formation: implications for periodic patterning. Dev Biol 196:11-23. Lande R. 1978. Evolutionary Mechanisms of Limb Loss in Tetrapods. Evolution 32:73-92. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. Laurell T, Nilsson D, Hofmeister W, Lindstrand A, Ahituv N, Vandermeer J, Amilon A, Anneren G, Arner M, Pettersson M, et al. 2014. Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease. Mol Genet Genomic Med 2:402-411. Lin CM, Jiang TX, Baker RE, Maini PK, Widelitz RB, Chuong CM. 2009. Spots and stripes: pleomorphic patterning of stem cells via p-ERK-dependent cell chemotaxis shown by feather morphogenesis and mathematical simulation. Dev Biol 334:369-382. Liu WY, Chang YM, Chen SC, Lu CH, Wu YH, Lu MY, Chen DR, Shih AC, Sheue CR, Huang HC, et al. 2013. Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination. Proc Natl Acad Sci U S A 110:3979-3984. Loftus SK, Larson DM, Watkins-Chow D, Church DM, Pavan WJ. 2001. Generation of RCAS vectors useful for functional genomic analyses. DNA Res 8:221-226. Mandler M, Neubuser A. 2004. FGF signaling is required for initiation of feather placode development. Development 131:3333-3343. Mardis ER. 2008a. The impact of next-generation sequencing technology on genetics. Trends Genet 24:133-141. Mardis ER. 2008b. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402. McDevitt D, Rosenberg M. 2001. Exploiting genomics to discover new antibiotics. Trends Microbiol 9:611-617. McKinnell IW, Turmaine M, Patel K. 2004. Sonic Hedgehog functions by localizing the region of proliferation in early developing feather buds. Dev Biol 272:76-88. Meinhardt H, Gierer A. 2000. Pattern formation by local self-activation and lateral inhibition. BioEssays : news and reviews in molecular, cellular and developmental biology 22:753-760. Metzker ML. 2005. Emerging technologies in DNA sequencing. Genome Res 15:1767-1776. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-628. Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, Tato P, Yu L, Burt DW, Bed'hom B, Tixier-Boichard M, et al. 2011. Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering. PLoS Biol 9:e1001028. Murray JR, Varian-Ramos CW, Welch ZS, Saha MS. 2013. Embryological staging of the Zebra Finch, Taeniopygia guttata. J Morphol 274:1090-1110. Ng CS, Chen CK, Fan WL, Wu P, Wu SM, Chen JJ, Lai YT, Mao CT, Lu MY, Chen DR, et al. 2015. Transcriptomic analyses of regenerating adult feathers in chicken. BMC Genomics 16:756. Noramly S, Freeman A, Morgan BA. 1999. beta-catenin signaling can initiate feather bud development. Development 126:3509-3521. Oh HM, Choi SC, Lee HS, Chun CH, Seo GS, Choi EY, Lee HJ, Lee MS, Yeom JJ, Choi SJ, et al. 2004. Combined action of extracellular signal-regulated kinase and p38 kinase rescues Molt4 T cells from nitric oxide-induced apoptotic and necrotic cell death. Free Radic Biol Med 37:463-479. Olivera-Martinez I, Viallet JP, Michon F, Pearton DJ, Dhouailly D. 2004. The different steps of skin formation in vertebrates. Int J Dev Biol 48:107-115. Ornitz DM, Itoh N. 2001. Fibroblast growth factors. Genome Biol 2:REVIEWS3005. Paznekas WA, Okajima K, Schertzer M, Wood S, Jabs EW. 1999. Genomic organization, expression, and chromosome location of the human SNAIL gene (SNAI1) and a related processed pseudogene (SNAI1P). Genomics 62:42-49. Pinaud R. 2010. Genome of a songbird unveiled. J Biol 9:19. Podulka S, Rohrbaugh RW, Bonney R. 2004. Handbook of bird biology. Ithaca, NY: Cornell Lab of Ornithology in association with Princeton University Press. Protas ME, Trontelj P, Patel NH. 2011. Genetic basis of eye and pigment loss in the cave crustacean, Asellus aquaticus. Proc Natl Acad Sci U S A 108:5702-5707. Prum RO. 2005. Evolution of the morphological innovations of feathers. J Exp Zool B Mol Dev Evol 304:570-579. Prum RO, Brush AH. 2002. The evolutionary origin and diversification of feathers. Q Rev Biol 77:261-295. Reimand J, Arak T, Vilo J. 2011. g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res 39:W307-315. Reimand J, Kull M, Peterson H, Hansen J, Vilo J. 2007. g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 35:W193-200. Sang H. 2004. Prospects for transgenesis in the chick. Mech Dev 121:1179-1186. Scholl FA, Dumesic PA, Barragan DI, Harada K, Bissonauth V, Charron J, Khavari PA. 2007. Mek1/2 MAPK kinases are essential for Mammalian development, homeostasis, and Raf-induced hyperplasia. Dev Cell 12:615-629. Schuster SC. 2008. Next-generation sequencing transforms today's biology. Nat Methods 5:16-18. Song HK, Lee SH, Goetinck PF. 2004. FGF-2 signaling is sufficient to induce dermal condensations during feather development. Dev Dyn 231:741-749. Starck JM, Ricklefs RE. 1998. Avian growth and development : evolution within the altricial-precocial spectrum. New York: Oxford University Press. Stern CD. 2004. The chick embryo--past, present and future as a model system in developmental biology. Mech Dev 121:1011-1013. Stern CD. 2005. The chick: A great model system becomes even greater. Developmental Cell 8:9-17. Strasser B, Mlitz V, Hermann M, Tschachler E, Eckhart L. 2015. Convergent evolution of cysteine-rich proteins in feathers and hair. BMC Evol Biol 15:82. Tao H, Yoshimoto Y, Yoshioka H, Nohno T, Noji S, Ohuchi H. 2002. FGF10 is a mesenchymally derived stimulator for epidermal development in the chick embryonic skin. Mech Dev 116:39-49. Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: a matter of depth. Genome Res 21:2213-2223. Terres JK, National Audubon Society. 1991. The Audubon Society encyclopedia of North American birds. New York: Wings Books : Distributed by Outlet Book Co. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. 2013. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31:46-53. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111. Vleck CM, Vleck D. 1987. Metabolism and energetics of avian embryos. J Exp Zool Suppl 1:111-125. Warnes GR, Bolker B, Bonebakker L, Gentleman R, Huber W, Liaw A, Lumley T, Maechler M, Magnusson A, Moeller S. 2009. gplots: Various R programming tools for plotting data. R package version 2. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, et al. 2010. The genome of a songbird. Nature 464:757-762. Wells KL, Hadad Y, Ben-Avraham D, Hillel J, Cahaner A, Headon DJ. 2012. Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens. BMC Genomics 13:257. Widelitz RB, Jiang TX, Lu J, Chuong CM. 2000. beta-catenin in epithelial morphogenesis: conversion of part of avian foot scales into feather buds with a mutated beta-catenin. Dev Biol 219:98-114. Widelitz RB, Jiang TX, Noveen A, Chen CW, Chuong CM. 1996. FGF induces new feather buds from developing avian skin. J Invest Dermatol 107:797-803. Wright MT. 2006. Birds of the world : recommended English names. London: Christopher Helm. Yue Z, Jiang TX, Wu P, Widelitz RB, Chuong CM. 2012. Sprouty/FGF signaling regulates the proximal-distal feather morphology and the size of dermal papillae. Dev Biol 372:45-54. Zann RA. 1996. The zebra finch : a synthesis of field and laboratory studies. Oxford ; New York: Oxford University Press. Zhang GJ, Li C, Li QY, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-1320. Zheng X, Zhou Z, Wang X, Zhang F, Zhang X, Wang Y, Wei G, Wang S, Xu X. 2013. Hind wings in Basal birds and the evolution of leg feathers. Science 339:1309-1312. Zhou Z, Zhang F. 2004. A precocial avian embryo from the Lower Cretaceous of China. Science 306:653. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/2690 | - |
dc.description.abstract | 鳥類可以分成晚熟與早熟鳥兩個大群,晚熟鳥的幼雛通常絨毛稀疏而皮膚裸露,早熟鳥則通常全身覆蓋著絨毛。一般認為,這種形態上的差異是跟環境的適應有關,但是背後的分子機制仍然不明朗。在本研究中,我以晚熟的錦花雀以及早熟的雞作為研究的模式物種。錦花雀的幼雛具有皮膚裸露的前背部,以及部份長有絨毛的後背部。藉由高通量的轉錄組定序與分析,我比較了前背部與後背部的基因表現,結果發現促進羽毛生長相關的基因SHH (sonic hedgehog)在後背部有較高的表現量。此外,資料分析也顯示FGF/MAPK訊息路徑可能跟前背部絨毛的生長抑制相關,而FGF16 (fibroblast growth factor 16)可能是這個訊息路徑的上游調控因子。將FGF16以病毒表現系統異位表現於雞胚胎的腿部,結果該部位的絨毛生長被抑制,出現類似錦花雀胚胎前背部的樣式,而且該部位SHH的表現量減少,又一個已知的羽毛抑制因子FGF10的表現量則增加。因此,我認為FGF16相關的分子訊息抑制了絨毛的生長,進而造成了錦花雀幼雛裸露的前背部。本研究闡述了早晚熟鳥之間絨毛生成可能的基因調控差異。 | zh_TW |
dc.description.abstract | Birds can be classified into altricial and precocial. The hatchlings of altricial birds are almost naked, whereas those of precocial birds are covered with natal down. This regulatory divergence is thought to reflect environmental adaptation, but the molecular basis of the divergence is unclear. To address this issue, I chose the altricial zebra finch and the precocial chicken as the model animals. Anatomical analysis revealed that zebra finch hatchlings showed suppressed natal down growth in anterior dorsal (AD) skin but partially down-covered posterior dorsal (PD) skin. A comparison of the transcriptomes of AD and PD skins revealed a higher expression level of the feather growth promoter SHH (sonic hedgehog) in PD skin than in AD skin. Moreover, the data suggested that the FGF/MAPK signaling pathway is involved in natal down growth suppression and that FGF16 (fibroblast growth factor 16) is an upstream signaling suppressor. Ectopic expression of FGF16 on chicken leg skin showed downregulation of SHH, upregulation of the feather growth suppressor FGF10, and suppression of feather bud elongation, similar to the phenotype found in zebra finch embryonic AD skin. Therefore, I propose that FGF16 related signals suppress natal down elongation and cause the naked AD skin in zebra finch. This study provides insights into the regulatory divergence in natal down formation between precocial and altricial birds. | en |
dc.description.provenance | Made available in DSpace on 2021-05-13T06:48:39Z (GMT). No. of bitstreams: 1 ntu-106-D98B44004-1.pdf: 3805636 bytes, checksum: 6f1b8784f4d719d848bd31e854e5840a (MD5) Previous issue date: 2017 | en |
dc.description.tableofcontents | ABSTRACT (Chinese) i
ABSTRACT (English) ii OUTLINE iii LIST OF FIGURES v LIST OF TABLES vii 1 Introduction 1 1.1 Background and significance 1 1.1.1 Feather diversity and bird diversity 1 1.1.2 Feather development and the molecular mechanisms 2 1.1.3 Altricial and precocial birds 3 1.1.4 Zebra finch and chicken as the altricial and the precocial model 6 1.2 Specific aims and experimental design 7 2 Materials and Methods 9 2.1 Ethics statement 9 2.2 Eggs and animals 9 2.3 Paraffin section and immunohistochemistry 9 2.4 Tissue total RNA isolation 10 2.5 Quantitative PCR 10 2.6 mRNA whole mount in situ hybridization 10 2.7 Stranded RNA sequencing 11 2.8 Data processing and reads mapping 11 2.9 Clustering analysis and identification of differentially expressed genes 12 2.10 Gene set enrichment and pathway analysis 13 2.11 Functional studies 13 3 Results 14 3.1 Two types of natal down formation in zebra finch embryos 14 3.2 Anterior dorsal interbud region thickening 18 3.3 Transcriptomes of AD and PD regions 24 3.4 Clusters of gene expression profiles and their functional enrichments 28 3.5 Differential SHH expression between Type I and II feather formations 32 3.6 FGF16 suppresses natal down growth and thickens the epithelium through the FGF/MAPK pathway 34 4 Discussion 42 SUMMARY AND PROSPECTIONS 46 REFERENCES 51 APPENDIX 60 CURRICULUM VITAE 75 | |
dc.language.iso | en | |
dc.title | 晚熟鳥錦花雀與早熟鳥雞在初生絨毛發育上基因調控之差異 | zh_TW |
dc.title | Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken | en |
dc.type | Thesis | |
dc.date.schoolyear | 105-1 | |
dc.description.degree | 博士 | |
dc.contributor.coadvisor | 李文雄(Wen-Hsiung Li) | |
dc.contributor.oralexamcommittee | 鄭旭辰(Hsu-Chen Cheng),林劭品,李壽先 | |
dc.subject.keyword | 早熟鳥,晚熟鳥,羽毛演化,絨羽,錦花雀, | zh_TW |
dc.subject.keyword | altricial bird,precocial bird,feather evolution,natal down,zebra finch, | en |
dc.relation.page | 77 | |
dc.identifier.doi | 10.6342/NTU201700010 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2017-01-18 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 生態學與演化生物學研究所 | zh_TW |
顯示於系所單位: | 生態學與演化生物學研究所 |
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