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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 游智凱(Jr-Kai Yu) | |
| dc.contributor.author | Kun-Lung Li | en |
| dc.contributor.author | 李坤龍 | zh_TW |
| dc.date.accessioned | 2021-06-16T16:34:27Z | - |
| dc.date.available | 2013-01-16 | |
| dc.date.copyright | 2013-01-16 | |
| dc.date.issued | 2012 | |
| dc.date.submitted | 2012-11-15 | |
| dc.identifier.citation | Abascal, F., Zardoya, R., Posada, D., 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105.
Abel, J., Haarmann-Stemmann, T., 2010. An introduction to the molecular basics of aryl hydrocarbon receptor biology. Biol. Chem. 391, 1235-1248. Aitola, M.H., Pelto-Huikko, M.T., 2003. Expression of Arnt and Arnt2 mRNA in developing murine tissues. J. Histochem. Cytochem. 51, 41-54. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J., 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. Auger, A. P., Tetel, M. J., McCarthy, M. M., 2000. Steroid receptor coactivator-1 (SRC-1) mediates the development of sex-specific brain morphology and behavior. Proc. Natl. Acad. Sci. U. S. A. 97, 7551-7555. Bai, J., Uehara, Y., Montell, D.J., 2000. Regulation of invasive cell behavior by taiman, a Drosophila protein related to AIB1, a steroid receptor coactivator amplified in breast cancer. Cell 103, 1047-1058. Bell-Pedersen, D., Cassone, V.M., Earnest, DJ., Golden, S.S., Hardin, P.E., Thomas, T.L., Zoran, M.J., 2005. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat. Rev. Genet. 6, 544-556. Berger, J., Senti, K.A., Senti, G., Newsome, T.P., Asling, B., Dickson, B.J., Suzuki, T., 2008. Systematic identification of genes that regulate neuronal wiring in the Drosophila visual system. PLoS Genet. 4, e1000085. Bertrand, S., Escriva, H., 2011. Evolutionary crossroads in developmental biology: amphioxus. Development 138, 4819-4830. Bourlat, S.J., Juliusdottir, T., Lowe, C.J., Freeman, R., Aronowicz, J., Kirschner, M., Lander, E.S., Thorndyke, M., Nakano, H., Kohn, A.B., Heyland, A., Moroz, L.L., Copley, R.R., Telford, M.J., 2006. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85-88. Brunskill, E.W., Ehrman, L.A., Williams, M.T., Klanke, J., Hammer, D., Schaefer, T.L., Sah, R., Dorn, G.W. 2nd, Potter, S.S., Vorhees, C.V., 2005. Abnormal neurodevelopment, neurosignaling and behaviour in Npas3-deficient mice. Eur. J. Neurosci. 22, 1265-1276. Cameron, R.A., Samanta, M., Yuan, A., He, D., Davidson, E., 2009. SpBase: the sea urchin genome database and web site. Nucleic Acids Res. 37(Database):D750- D754. Chen, Y., Ding, Y., Zhang, Z., Wang, W., Chen, J.Y., Ueno, N., Mao, B., 2011. Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes. J. Genet. Genomics 38, 577-584. Crews, S.T., 1998. Control of cell lineage-specific development and transcription by bHLH-PAS proteins. Genes Dev. 12, 607-620. Duncan, D.M., Burgess, E.A., Duncan, I., 1998. Control of distal antennal identity and tarsal development in Drosophila by spineless-aristapedia, a homolog of the mammalian dioxin receptor. Genes Dev. 12, 1290-1303. Dunwoodie, S.L., 2009. The role of hypoxia in development of the mammalian embryo. Dev. Cell 17, 755-773. Ema, M., Morita, M., Ikawa, S., Tanhaka, M., Gotoh, O., Saijoh, S., Fujii, H., Hamada, H., Fujii-Kuriyama, Y., 1996. Two new members of murine Sim gene family are transcriptional repressors and show different patterns during mouse embryogenesis. Mol. Cell. Biol. 16, 5865-5875. Emmons, R.B., Duncan, D., Estes, P.A., Kiefel, P., Mosher, J.T., Sonnenfeld, M., Ward, M.P., Duncan, I., Crews, S.T., 1999. The spineless-aristapedia and tango bHLH-PAS proteins interact to control antennal and tarsal development in Drosophila. Development 126, 3937-3945. Erbel-Sieler, C., Dudley, C., Zhou, Y., Wu, X., Estill, S.J., Han, T., Diaz-Arrastia, R., Brunskill, E.W., Potter, S.S., McKnight, S.L., 2004. Behavioral and regulatory abnormalities in mice deficient in the NPAS1 and NPAS3 transcription factors. Proc. Natl. Acad. Sci. U. S. A. 101, 13648-13653. Fan, C.M., Kuwana, E., Bulfone, A., Fletcher, C.F., Copeland, N.G., Jenkins, N.A., Crews, S., Martinez, S., Puelles, L., Rubenstein, J.L., Tessier-Lavigne, M., 1996. Expression patterns of two murine homologs of Drosophila single-minded suggest possible roles in embryonic patterning and in the pathogenesis of Down syndrome. Mol. Cell. Neurosci. 7, 1-16. Ferre-D’Amare, A.R., Prendergast, G.C., Ziff, E.B., Burley, S.K., 1993. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363, 38-45. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., Postlethwait, J., 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545. Goldstone, J.V., Hamdoun, A., Cole, B.J., Howard-Ashby, M., Nebert, D.W., Scally, M., Dean, M., Epel, D., Hahn, M.E., Stegeman, J.J., 2006. The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome. Dev. Biol. 300, 366-384. Gorr, T. A., Tomita, T., Wappner, P., Bunn, H.F., 2004. Regulation of Drosophila hypoxia-inducible factor (HIF) activity in SL2 cells: identification of a hypoxia-induced variant isoform of the HIFalpha homolog gene similar. J. Biol. Chem. 279, 36048-36058. Hahn, M.E., Allan, L.L., Sherr, D.H., 2009. Regulation of constitutive and inducible AHR signaling: complex interactions involving the AHR repressor. Biochem. Pharmacol. 77, 485-497. Hall, T. A., 1999. BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98. Hampton-Smith, R. J., Peet, D.J., 2009. From polyps to people: a highly familiar response to hypoxia. Ann. N. Y. Acad. Sci. 1177, 19-29. Hirakow, R., Kajita, N., 1991. Electron microscopic study of the development of amphioxus, Branchiostoma belcheri tsingtauense: the gastrula. J. Morphol. 207, 37-52. Hirakow, R., Kajita, N., 1994. Electron microscopic study of the development of amphioxus, Branchiostoma belcheri tsingtauense: the neurula and larva. Acta Anat. Nippon 69, 1-13. Holland, L.Z., 2005. Non-neural ectoderm is really neural: evolution of developmental patterning mechanisms in the non-neural ectoderm of chordates and the problem of sensory cell homologies. J. Exp. Zool. B Mol. Dev. Evol. 304, 304-323. Holland, L. Z., Holland, P. W. H., Holland, N. D., 1996. Revealing homologies between body parts of distantly related animals by in situ hybridization to developmental genes: amphioxus versus vertebrates. In J. D. Ferraris and S. R. Palumbi (eds.). Molecular Zoology: Advances, Strategies, and Protocols. Wiley, New York, pp. 267-282, 473-483. Huang, X., Powell-Coffman, J.A., Jin, Y., 2004. The AHR-1 aryl hydrocarbon receptor and its co-factor the AHA-1 aryl hydrocarbon receptor nuclear translocator specify GABAergic neuron cell fate in C. elegans. Development 131, 819-828. Hughes, A. L., Friedman, R., 2005. Loss of ancestral genes in the genomic evolution of Ciona intestinalis. Evol. Dev. 7, 196 -200. Isaac, D.D., Andrew, D.J., 1996. Tubulogenesis in Drosophila: a requirement for the trachealess gene product. Genes Dev. 10, 103-117. Iyer, N.V., Kotch, L.E., Agani, F., Leung, S.W., Laughner, E., Wenger, R.H., Gassmann, M., Gearhart, J.D., Lawler, A.M., Yu, A.Y., Semenza, G.L., 1998. Cellular and developmental control of O2 homeostasis by hypoxia-inducible factor 1 alpha. Genes Dev. 12, 149-162. Jain, S., Maltepe, E., Lu, M.M., Simon, C., Bradfield, C.A., Expression of ARNT, ARNT2, HIF1 alpha, HIF2 alpha and Ah receptor mRNAs in the developing mouse. Mech Dev. 73, 117-123. Jiang, L., Crews, S.T., 2003. The Drosophila dysfusion basic helix-loop-helix (bHLH)-PAS gene controls tracheal fusion and levels of the trachealess bHLH-PAS protein. Mol. Cell. Biol. 23, 5625-5637. Jiang, L., Crews, S. T., 2006. dysfusion transcriptional control of Drosophila tracheal migration, adhesion, and fusion. Mol. Cell. Biol. 26, 6547-6556. Jones, D.T., Taylor, W.R., Thornton, J.M., 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282. Kaelin, W.G. Jr, Ratcliffe, P.J., 2008. Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol. Cell 30, 393-402. Ko, C.H., Takahashi, J.S., 2006. Molecular components of the mammalian circadian clock. Hum. Mol. Genet. 15, R271-R277. Konopova, B., Jindra, M., 2007. Juvenile hormone resistance gene Methoprene-tolerant controls entry into metamorphosis in the beetle Tribolium castaneum. Proc. Natl. Acad. Sci. U. S. A. 104, 10488-10493. Lahvis, G.P., Lindell, S.L., Thomas, R.S., McCuskey, R.S., Murphy, C., Glover, E., Bentz, M., Southard, J., Bradfield, C.A., 2000. Portosystemic shunting and persistent fetal vascular structures in aryl hydrocarbon receptor-deficient mice. Proc. Natl. Acad. Sci. U. S. A. 97, 10442-10447. Langeland, J.A., Tomsa, J.M., Jackman, W.R. Jr, Kimmel, C.B., 1998. An amphioxus snail gene: expression in paraxial mesoderm and neural plate suggests a conserved role in patterning the chordate embryo. Dev. Genes Evol. 208, 569-577. Ledent, V., Vervoort, M., 2001. The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res. 11, 754-770. Ledent, V., Paquet, O., Vervoort, M., 2002. Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol. 3, 0030.1-0030.18. Levesque, B.M., Zhou, S., Shan, L., Johnston, P., Kong, Y., Degan, S., Sunday, M.E., NPAS1 regulates branching morphogenesis in embryonic lung. Am. J. Respir, Cell Mol. Biol. 36, 427-434. Loenarz, C., Coleman, M.L., Boleininger, A., Schierwater, B., Holland, P.W., Ratcliffe, P.J., Schofield, C.J., 2011. The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens. EMBO Rep. 12, 63-70. Lu, T.M., Luo, Y.J., Yu, J.K., 2012. BMP and Delta/Notch signaling control the development of amphioxus epidermal sensory neurons: insights into the evolution of the peripheral sensory system. Development 139, 2020-2030. Massari, M.E., Murre, C., 2000. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell. Biol. 20, 429-440. Mazet, F., Shimeld, S.M., 2002. The evolution of chordate neural segmentation. Dev. Biol. 251, 258-270. McIntosh, B.E., Hogenesch, J.B., Bradfield, C.A., 2010. Mammalian Per-Arnt-Sim proteins in environmental adaptation. Annu. Rev. Physiol. 72, 625-645. Meijer, O.C., Steenbergen, P.J., De Kloet, E.R., 2000. Differential expression and regional distribution of steroid receptor coactivators SRC-1 and SRC-2 in brain and pituitary. Endocrinology 141, 2192-2199. Meulemans, D., Bronner-Fraser, M., 2007. The amphioxus SoxB family: implications for the evolution of vertebrate placodes. Int. J. Biol. Sci. 3, 356-364. Michaud, J.L., Rosenquist, T., May, N.R., Fan, C.M., 1998. Development of neuroendocrine lineages requires the bHLH-PAS transcription factor SIM1. Genes Dev. 12, 3264-3275. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, pp. 1-8. Minamoto, T., Hanai, S., Kadota, K., Oishi, K., Matsumae, H., Fujie, M., Azumi, K., Satoh, N., Satake, M., Ishida, N., Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption. J. Biochem. 147, 175-184. Misiti, S., Koibuchi, N., Bei, M., Farsetti, A., Chin, W.W., 1999. Expression of steroid receptor coactivator-1 mRNA in the developing mouse embryo: a possible role in olfactory epithelium development. Endocrinology 140, 1957-1960. Nambu, J.R., Franks, R.G., Hu, S., Crews, S.T., 1990. The single-minded gene of Drosophila is required for the expression of genes important for the development of CNS midline cells. Cell 63, 63-75. Nambu, J.R., Lewis, J.O., Wharton, K.A., Crews, S.T., 1991. The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. Cell 67, 1157-1167. Ooe, N., Saito, K., Mikami, N., Nakatuka, I., Kaneko, H., 2004. Identification of a novel basic helix-loop-helix-PAS factor, NXF, reveals a Sim2 competitive, positive regulatory role in dendritic-cytoskeleton modulator drebrin gene expression. Mol. Cell. Biol. 24, 608-616. Ooe, N., Motonaga, K., Kobayashi, K., Saito, K., Kaneko, H., 2009a. Functional characterization of basic helix-loop-helix-PAS type transcription factor NXF in vivo: putative involvement in an 'on demand' neuroprotection system. J. Biol. Chem. 284, 1057-1063. Ooe, N., Saito, K., Kaneko, H., 2009b. Characterization of functional heterodimer partners in brain for a bHLH-PAS factor NXF. Biochim. Biophys. Acta. 1789, 192-197. Panopoulou, G., Poustka, A.J., 2005. Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis. Trends Genet. 21, 559-567. Ploski, J.E., Monsey, M.S., Nguyen, T., DiLeone, R.J., Schafe, G.E., 2011. The neuronal PAS domain protein 4 (Npas4) is required for new and reactivated fear memories. PLoS One 6, e23760. Probst, M.R., Reisz-Porszasz, S., Agbunag, R.V., Ong, M.S., Hankinson, O., 1993. Role of the aryl hydrocarbon receptor nuclear translocator protein in aryl hydrocarbon (dioxin) receptor action. Mol. Pharmacol. 44, 511-518. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E.L., Eddy, S.R., Bateman, A., Finn, R.D., 2012. The Pfam protein families database. Nucleic Acids Res. 40(Database), D290-D301. Putnam, N.H., Butts, T., Ferrier, D.E., Furlong, R.F., Hellsten, U., Kawashima, T., Robinson-Rechavi, M., Shoguchi, E., Terry, A., Yu, J.K., Benito-Gutierrez, E.L., Dubchak, I., Garcia-Fernandez, J., Gibson-Brown, J.J., Grigoriev, I.V., Horton, A.C., de Jong, P.J., Jurka, J., Kapitonov, V.V., Kohara, Y., Kuroki, Y., Lindquist, E., Lucas, S., Osoegawa, K., Pennacchio, L.A., Salamov, A.A., Satou, Y., Sauka-Spengler, T., Schmutz, J., Shin-I, T., Toyoda, A., Bronner-Fraser, M., Fujiyama, A., Holland, L.Z., Holland, P.W., Satoh, N., Rokhsar, D.S. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064-71. Qin, H., Powell-Coffman, J.A., 2004. The Caenorhabditis elegans aryl hydrocarbon receptor, AHR-1, regulates neuronal development. Dev. Biol. 270, 64-75. Reitzel, A.M., Behrendt, L., Tarrant, A.M., 2010. Light entrained rhythmic gene expression in the sea anemone Nematostella vectensis: the evolution of the animal circadian clock. PLoS One 5, e12805. Satou, Y., Imai, K.S., Levine, M., Kohara, Y., Rokhsar, D., Satoh, N., 2003. A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev. Genes Evol. 213, 213-221. Satou, Y., Wada, S., Sasakura, Y., Satoh, N., 2008. Regulatory genes in the ancestral chordate genomes. Dev. Genes Evol. 218, 715-721. Schmidt, J.V., Su, G.H., Reddy, J.K., Simon, M.C., Bradfield, C.A., 1996. Characterization of a murine Ahr null allele: involvement of the Ah receptor in hepatic growth and development. Proc. Natl. Acad. Sci. U. S. A. 93, 6731-6736. Schomerus, C., Korf, H.W., Laedtke, E., Moret, F., Zhang, Q., Wicht, H. 2008. Nocturnal behavior and rhythmic period gene expression in a lancelet, Branchiostoma lanceolatum. J. Biol. Rhythms 23, 170-181. Shamblott, M.J., Bugg, E.M., Lawler, A.M., Gearhart, J.D., 2002. Craniofacial abnormalities resulting from targeted disruption of the murine Sim2 gene. Dev. Dyn. 224, 373-380. Simionato, E., Ledent, V., Richards, G., Thomas-Chollier, M., Kerner, P., Coornaert, D., Degnan, B. M., Vervoort, M., 2007. Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics. BMC Evol. Biol. 7, 33. Sonnenfeld, M., Ward, M., Nystrom, G., Mosher, J., Stahl, S., Crews, S., 1997. The Drosophila tango gene encodes a bHLH-PAS protein that is orthologous to mammalian Arnt and controls CNS midline and tracheal development. Development 124, 4571-4582. Srivastava, M., Begovic, E., Chapman, J., Putnam, N.H., Hellsten, U., Kawashima, T., Kuo, A., Mitros, T., Salamov, A., Carpenter, M.L., Signorovitch, A.Y., Moreno, M.A., Kamm, K., Grimwood, J., Schmutz, J., Shapiro, H., Grigoriev, I.V., Buss, L.W., Schierwater, B., Dellaporta, S.L., Rokhsar, D.S., 2008. The Trichoplax genome and the nature of placozoans. Nature 454, 955-960. Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. Stamatakis, A., Hoover, P., Rougemont, J., 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57, 758-771. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739. Tassy, O., Dauga, D., Daian, F., Sobral, D., Robin, F., Khoueiry, P., Salgado, D., Fox, V., Caillol, D., Schiappa, R., Laporte, B., Rios, A., Luxardi, G., Kusakabe, T., Joly, J.S., Darras, S., Christiaen, L., Contensin, M., Auger, H., Lamy, C., Hudson, C., Rothbacher, U., Gilchrist, M.J., Makabe, K.W., Hotta, K., Fujiwara, S., Satoh, N., Satou, Y., Lemaire, P., 2010. The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Genome Res. 20, 1459-1468. Taylor, B.L., Zhulin, I.B., 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63, 479-506. Tei, H., Okamura, H., Shigeyoshi, Y., Fukuhara, C., Ozawa, R., Hirose, M., Sakaki, Y., 1997. Circadian oscillation of a mammalian homologue of the Drosophila period gene. Nature 389, 512-516. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680. Tu, Q., Cameron, R.A., Worley, K.C., Gibbs, R.A., Davidson, E.H., 2012. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res. 22, 2079-2087. Wang, Y.B., Chen, S.H., Lin, C.Y., Yu, J.K., 2012. EST and transcriptome analysis of cephalochordate amphioxus--past, present and future. Brief. Funct. Genomics. 11, 96-106. Wicht, H., Laedtke, E., Korf, H.W., Schomerus, C., 2010. Spatial and temporal expression patterns of Bmal delineate a circadian clock in the nervous system of Branchiostoma lanceolatum. J. Comp. Neurol. 518, 1837-1846. Wilk, R., Weizman, I., Shilo, B.Z., 1996. trachealess encodes a bHLH-PAS protein that is an inducer of tracheal cell fates in Drosophila. Genes Dev. 10, 93-102. Wu, H.R., Chen, Y.T., Su, Y.H., Luo, Y.J., Holland, L.Z., Yu, J.K., 2011. Asymmetric localization of germline markers Vasa and Nanos during early development in the amphioxus Branchiostoma floridae. Dev. Biol. 353, 147-159. Xu, J., Li, Q., 2003. Review of the in vivo functions of the p160 steroid receptor coactivator family. Mol. Endocrinol. 17, 1681-1692. Yamashita, T., Ohneda, O., Nagano, M., Iemitsu, M., Makino, Y., Tanaka, H., Miyauchi, T., Goto, K., Ohneda, K., Fujii-Kuriyama, Y., Poellinger, L., Yamamoto, M., 2008. Abnormal heart development and lung remodeling in mice lacking the hypoxia-inducible factor-related basic helix-loop-helix PAS protein NEPAS. Mol. Cell. Biol. 28, 1285-1297. Ye, R., Selby, C.P., Ozturk, N., Annayev, Y., Sancar, A., 2011. Biochemical analysis of the canonical model for the mammalian circadian clock. J. Biol. Chem. 286, 25891-25902. Yu, J.K.S., Holland, L.Z., 2009. Extraction of RNA from small amounts of amphioxus embryos for cDNA synthesis by RT-PCR. CSH Protoc. doi:10.1101/pdb.prot5289. Yu, J.K., Wang, M.C., Shin-I, T., Kohara, Y., Holland, L.Z., Satoh, N., Satou, Y., 2008. A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae. Dev. Genes Evol. 218, 723-727. Zhou, Y.D., Barnard, M., Tian, H., Li, X., Ring, H.Z., Francke, U., Shelton, J., Richardson, J., Russell, D.W., McKnight, S.L., 1997. Molecular characterization of two mammalian bHLH-PAS domain proteins selectively expressed in the central nervous system. Proc. Natl. Acad. Sci. U. S. A. 94, 713-718. Zhou, S., Degan, S., Potts, E.N., Foster, W.M., Sunday, M.E., 2009. NPAS3 is a trachealess homolog critical for lung development and homeostasis. Proc. Natl. Acad. Sci. U. S. A. 106, 11691-11696. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/63315 | - |
| dc.description.abstract | bHLH-PAS轉錄因子廣泛存在於原口動物與後口動物各動物門，它們參與許多重要的發育與生理功能，包含中樞神經系統的區域分化、氣管生成、低氧感應、芳香烴感應，以及調控生物時鐘等。雖然它們的功能在無脊椎模式物種與脊椎動物之間有明顯的差異，目前對於這些基因功能的演化所知仍甚少。為瞭解這些基因在脊索動物的演化，我以頭索動物文昌魚 (Branchiostoma floridae) 作為材料，由既有的基因組和基因模型 (gene models) 中鑑別文昌魚的bHLH-PAS基因。我的結果顯示：文昌魚擁有至少十個bHLH-PAS基因，其中九個可以被歸類到已知的直系同源基因家族。再者，由獲得的cDNA與gene models之間的差異，可瞭解到既有的gene models無法完全正確地預測真實的基因序列。最後，我使用即時聚合酶鏈鎖反應與核酸原位雜交方法，檢驗了文昌魚胚胎發育過程中這些基因的表現模式，發現BfArnt、BfNcoa、BfSim、BfHifα等基因的表現模式與脊椎動物的同源基因表現模式非常相似，這可能表示它們的功能保守；但是另一些基因，如BfAhr與BfNpas4，其表現模式與脊椎動物同源基因有明顯差異，這可能表示這些基因的功能在兩個演化分支分歧之後發生改變。脊椎動物擁有多個旁系同源的bHLH-PAS基因，這些基因可能是來自脊椎動物的全基因組複製，我比較這些旁系同源基因的表現模式與功能，推論功能的分化或新功能的獲得可能可以解釋脊椎動物所擁有的多個旁系同源基因的功能歧異性。 | zh_TW |
| dc.description.abstract | The bHLH-PAS transcription factors are found in both protostomes and deuterostomes. They are involved in many developmental and physiological processes including the regional differentiation of the central nervous system, tube-formation, hypoxia signaling, aromatic hydrocarbon sensing, and circadian rhythm regulation. Although some of their functions are apparently different between model protostomes and vertebrates, little has been known about the evolution of their functions. To understand the evolution of these genes in chordates, I manually annotated bHLH-PAS genes of the basal chordate amphioxus (Branchiostoma floridae) from the draft genome database. My results show that amphioxus has at least 10 bHLH-PAS genes, 9 of which can be assigned to known orthologous families. Moreover, the comparisons of cDNA sequences and gene models show that current amphioxus gene models may not correctly predict the true coding sequence. Finally, I examined the developmental expression patterns of these amphioxus bHLH-PAS genes by quantitative polymerase chain reaction and in situ hybridization. I found that BfArnt, BfNcoa, BfSim, and BfHifα are expressed in similar patterns compared to their vertebrate homologues, suggesting that their functions may be conserved. On the other hand, BfAhr and BfNpas4 are expressed with different patterns between amphioxus and vertebrates. This might imply functional changes after the divergence of cephalochordates and vertebrates. Since vertebrates have multiple bHLH-PAS paralogues that may result from whole genome duplications, I compared the expression patterns and the functions of these paralogues. I suggest that neo- or subfunctionalization of the duplicated paralogues may explain the functional divergence of bHLH-PAS genes in the vertebrate lineage. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T16:34:27Z (GMT). No. of bitstreams: 1 ntu-101-R99241204-1.pdf: 4102123 bytes, checksum: 0a3759c2854ddec71fd0d76cb1d59113 (MD5) Previous issue date: 2012 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
謝辭 ii 摘要 iii Abstract iv 目錄 v 圖目錄 vi 表目錄 vii Introduction 1 Materials and Methods 6 Identification and sequences acquisition of amphioxus bHLH-PAS genes 6 Domain comparison and phylogenetic analysis 9 Comparisons of obtained cDNA assemblies to corresponding genomic scaffolds and gene models 11 Animal collection 12 Quantitative PCR (Q-PCR) 12 In situ hybridization and photography 14 Results 17 Identification of amphioxus bHLH-PAS genes 17 Conserved domains of bHLH-PAS proteins 18 Phylogenetic analyses 20 Comparisons of amphioxus bHLH-PAS cDNA to the existing genomic scaffolds and gene models 21 Temporal and spatial expression pattern of each bHLH-PAS gene 29 Discussion 38 Existence of 10 bHLH-PAS genes in B. floridae genome and the evolution of bHLH-PAS families in chordates 38 Advantages and limitations of using B. floridae gene models and the cDNA/EST resource to identify genes of interest 42 Gene expression and possible functions of bHLH-PAS genes 44 References 57 | |
| dc.language.iso | en | |
| dc.subject | bHLH轉錄因子 | zh_TW |
| dc.subject | Branchiostoma floridae | zh_TW |
| dc.subject | 分子親緣 | zh_TW |
| dc.subject | 胚胎發育 | zh_TW |
| dc.subject | 基因演化 | zh_TW |
| dc.subject | 文昌魚 | zh_TW |
| dc.subject | embryonic development | en |
| dc.subject | gene evolution | en |
| dc.subject | amphioxus | en |
| dc.subject | Branchiostoma floridae | en |
| dc.subject | molecular phylogeny | en |
| dc.subject | bHLH-PAS transcription factors | en |
| dc.title | 頭索動物文昌魚bHLH-PAS基因之研究 | zh_TW |
| dc.title | The bHLH-PAS genes in the cephalochordate amphioxus Branchiostoma floridae | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 101-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 陳韋仁(Wei-Jen Chen),蘇怡璇(Yi-Hsien Su) | |
| dc.subject.keyword | bHLH轉錄因子,基因演化,文昌魚,Branchiostoma floridae,分子親緣,胚胎發育, | zh_TW |
| dc.subject.keyword | bHLH-PAS transcription factors,gene evolution,amphioxus,Branchiostoma floridae,molecular phylogeny,embryonic development, | en |
| dc.relation.page | 102 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2012-11-16 | |
| dc.contributor.author-college | 理學院 | zh_TW |
| dc.contributor.author-dept | 海洋研究所 | zh_TW |
| 顯示於系所單位： | 海洋研究所 | |
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