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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 蕭超隆(Chiao-long Hsiao) | |
| dc.contributor.author | Yi-Shan Lan | en |
| dc.contributor.author | 藍以珊 | zh_TW |
| dc.date.accessioned | 2022-11-23T09:02:02Z | - |
| dc.date.available | 2021-11-03 | |
| dc.date.available | 2022-11-23T09:02:02Z | - |
| dc.date.copyright | 2021-11-03 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-10-22 | |
| dc.identifier.citation | 1. T. Chaillou, T. J. Kirby, J. J. McCarthy, Ribosome biogenesis: emerging evidence for a central role in the regulation of skeletal muscle mass. Journal of cellular physiology 229, 1584–1594 (2014). 2. A. Pyle, Metal ions in the structure and function of RNA. JBIC Journal of Biological Inorganic Chemistry 7, 679–690 (2002). 3. A. Tissières, J. Watson, D. Schlessinger, B. Hollingworth, Ribonucleoprotein particles from Escherichia coli. Journal of Molecular Biology 1, 221–233 (1959). 4. T. R. Cech, The ribosome is a ribozyme. Science 289, 878–879 (2000). 5. A. Harish, G. Caetano-Anolles, Ribosomal history reveals origins of modern protein synthesis. PloS one 7, e32776 (2012). 6. A. S. Petrov et al., History of the ribosome and the origin of translation. Proceedings of the National Academy of Sciences 112, 15396–15401 (2015). 7. J. C. Bowman, N. V. Hud, L. D. Williams, The ribosome challenge to the RNA world. Journal of molecular evolution 80, 143–161 (2015). 8. S. Wright (1945) Tempo and mode in evolution: a critical review. (JSTOR). 9. C. R. Woese, G. E. Fox, Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences 74, 5088–5090 (1977). 10. C. R. Woese, Bacterial evolution. Microbiological reviews 51, 221-271 (1987). 11. N. Arisue et al., Comparative Analysis of the Ribosomal Componentsof the Hydrogenosome-Containing Protist, Trichomonas vaginalis. Journal of molecular evolution 59, 59–71 (2004). 12. G. Caetano-Anollés, Evolved RNA secondary structure and the rooting of the universal tree of life. Journal of molecular evolution 54, 333–345 (2002). 13. C. R. Bernier et al., RiboVision suite for visualization and analysis of ribosomes. Faraday discussions 169, 195–207 (2014). 14. K. Bokov, S. V. Steinberg, A hierarchical model for evolution of 23S ribosomal RNA. Nature 457, 977–980 (2009). 15. R. Rakauskaitė, J. D. Dinman, rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance. Nucleic acids research 36, 1497–1507 (2008). 16. I. V. Velichutina et al., Mutations in helix 27 of the yeast Saccharomyces cerevisiae 18S rRNA affect the function of the decoding center of the ribosome. Rna 6, 1174–1184 (2000). 17. J. S. Lodmell, A. E. Dahlberg, A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277, 1262–1267 (1997). 18. H. M. Berman et al., The protein data bank. Nucleic acids research 28, 235–242 (2000). 19. J. A. Dunkle et al., Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science 332, 981–984 (2011). 20. M. Selmer et al., Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006). 21. D. J. Klein, T. M. Schmeing, P. B. Moore, T. A. Steitz, The kink‐turn: a new RNA secondary structure motif. The EMBO journal 20, 4214–4221 (2001). 22. A. Ben-Shem et al., The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334, 1524–1529 (2011). 23. A. M. Anger et al., Structures of the human and Drosophila 80S ribosome. Nature 497, 80–85 (2013). 24. R. K. Koripella et al., Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance. Nature Communications 12, 1–13 (2021). 25. A. Dereeper et al., Phylogeny. fr: robust phylogenetic analysis for the non-specialist. Nucleic acids research 36, W465–W469 (2008). 26. J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular biology and evolution 17, 540–552 (2000). 27. S. Guindon et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology 59, 307–321 (2010). 28. Z. Yang, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular evolution 39, 306–314 (1994). 29. D. M. Hillis, J. J. Bull, An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic biology 42, 182–192 (1993). 30. A. S. Petrov et al., Evolution of the ribosome at atomic resolution. Proceedings of the National Academy of Sciences 111, 10251–10256 (2014). | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/79502 | - |
| dc.description.abstract | 核醣體是生物體內的廣泛存在的轉譯機器，在核糖體內存在核糖體核糖核酸 (rRNA)，其擁有各類核糖核酸模體 (motif)使其被摺疊成複雜的球形構造，其中A-helix是在核糖體核糖核酸中最常出現的模體。核糖體中的A-helix構建出縱橫交錯的結構網路並支持肽基轉移中心 (PTC)，理解核糖體的架構可以幫助人解構生命的起源。在這裡，我開發了一種算法來產生一個數學的公式，此公式可以用來描述核糖體的架構。我計算了每個核醣體 A-helix到核醣體質心的幾何距離 (A-Rcom)，令人驚訝的是，A-Rcom 的分佈可以擬合到非線性模型中，每個核醣體結構都可以用數學方法描述。細菌、古細菌、真核核醣體符合擬合方程以保留核醣體結構。擬合方程使我能夠按時間重述核醣體結構的進化過程，此外，核醣體內A-helix的生物信息可以通過構建核醣體結構系統發育樹（RAP 樹）來進行系統發育研究。 RAP 樹的結果暗示核醣體的進化是一種量子進化。 | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-23T09:02:02Z (GMT). No. of bitstreams: 1 U0001-0410202109111800.pdf: 23796788 bytes, checksum: 64efd13ea0b91083e81e765702f7ee67 (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | 口試委員會審定書 i 謝誌 ii List of Figures iv List of Tables iv 中文摘要 v Abstract: vi Chapter 1. Introduction 1 1.1 The origin of life and the ribosome 1 1.2 The evolutionary studies of the ribosome 1 1.3 The A-helix motif of the ribosome 3 Chapter 2. Methods and Materials 4 2.1 Structural data quality and data access 4 2.2 DcomR algorithm development 5 2.3 Non-linear fitting 6 2.4 Binned sequence alignment 6 Chapter 3. Results 8 3.1 The ribosome architecture model. 8 3.2 Binned sequence alignment 12 Chapter 4. Discussion 15 4.1 DcomR algorithm and ribosomal architecture model. 15 4.2 Ribosome evolution 19 4.3 Binned sequence alignment 23 Chapter 5. Future works 25 References. 26 Appendix I. 28 Appendix II. 37 | |
| dc.language.iso | en | |
| dc.title | 核糖體架構與演化之研究 | zh_TW |
| dc.title | The study of the architecture and evolution of the ribosome | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 冀宏源(Hsin-Tsai Liu),張震東(Chih-Yang Tseng) | |
| dc.subject.keyword | 核醣體,A-螺旋基序,核醣體結構,非線性擬合,系統發育,量子進化, | zh_TW |
| dc.subject.keyword | the ribosome,A-helix motif,ribosomal architecture,nonlinear fitting,phylogeny,quantum evolution, | en |
| dc.relation.page | 47 | |
| dc.identifier.doi | 10.6342/NTU202103525 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-10-22 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科學研究所 | zh_TW |
| 顯示於系所單位： | 生化科學研究所 | |
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