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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.author | Chen-Hsin Yu | en |
| dc.contributor.author | 餘承欣 | zh_TW |
| dc.date.accessioned | 2021-07-01T08:12:52Z | - |
| dc.date.available | 2021-07-01T08:12:52Z | - |
| dc.date.issued | 2003 | |
| dc.identifier.citation | Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. Available at http://www.ncbi.nlm.nih.gov/BLAST/.
Amann, R. I., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169. Barcenilla, A., S. E. Pryde, J. C. Martin, S. H. Duncan, C. S. Stewart, C. Henderson, and H. J. Flint. 2000. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66:1654-1661. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler. 2000. GenBank. Nucleic Acids Res. 28:15-18. Bonnet, R., A. Suau, J. Dor?, G R. Gibson, and M. D. Collins. 2002. Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int. J. Syst. Evol. Microbiol. 52:757-763. Bonnie, L. M., J. R. Cole, T. G. Lilburn, C. T. Parker, J. P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29: 173-174. Borneman, J., and E. W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:2647-2653. Brunk, C. F., E. Avaniss-Aghajani, and C. A. Brunk. 1996. A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Appl. Environ. Microbiol. 62:872-879. Clement, M., D. Posada, and K. A. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9:1657-1659. Daly, K., C. S. Stewart, H. J. Flint, and S. P. Shirazi-Beechey. 2001. Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol. Ecol. 38:141-151. Deplancke, B., and H. R. Gaskin. 2001. Microbial modulation of innate defense: goblet cells and the intestinal mucus layer. Am. J. Clin. Nutr. 73:1131s-1141s. Devereux, R., and G. W. Mundfrom. 1994. A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment. Appl. Environ. Microbiol. 60:3437-3439. Escherich, T. 1885. The intestinal bacteria of the neonate and breast-fed infant. Forschritte der medizin, vol. 3. Featured in Rev. Infect. Dis. 10:1220-1225, 1988. Falk, P. G., L. V. Hooper, T. Midtvedt and J. I. Gordon. 1998. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 62:1157-1170. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47:49-55. Fischer, S. G., and L. S. Lerman. 1979. Length-independent separation of DNA restriction fragments in two dimentional gel electrophoresis. Cell 16:191-200. Ganz, T. 2003. Gut defence. Nature 422:478-479. Giovannoni, S. L., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso sea bacterioplankton. Nature 345:60-63. Giraud, A., I. Matic, O. Tenaillon, A. Clara, M. Radman, M. Fons, and F. Taddei. 2001. Costs and benefits of high mutation rates: Adaptation of bacteria in the mouse gut. Science 291:2606-2608. Godon, J. J., E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta. 1997. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63:2802-2813. Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrica 40:237-264. Hiraishi, A., M. Iwasaki, and H. Shinjo. 2000. Terminal restriction pattern analysis of 16S rRNA genes for the characterization of bacterial communities of activates sludge. J. Biosci. Bioeng. 90: 148-156. Hooper L. V., and J. I. Gordon. 2001. Commensal host-bacterial relationships in the gut. Science 292:1115-1118. Hooper L. V., M. H. Wong, A. Thelin, L. Hansson, P. G. Falk, and J. I. Gordon. 2001. Molecular analysis of commensal host-bacterial relationships in the intestine. Science 291:881-884. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921. Jones, J. G. 1977. The effect of environmental factors on estimated viable and total populations of planktonic bacteria in lakes and experimental enclosures. Freshwater Biol. 7:67-91. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. Kogure, K. U., U. Simidu, and N. Taga. 1980. Distribution of viable marine bacteria in neritic seawater around Japan. Can. J. Microbiol. 26:318-323. Koski, L. B. and G. B. Golding. 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52:540-542. Langendijk, P. S., F. Schut, G. J. Janse, G. C. Raangs, G. R. Kamphuis, M. H. Wilkenson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA- targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:3069-3075. Leser, T. D., J. Z. Amenuvor, T. K. Jensen, R. H. Lindecrona, M. Boye, and K. M?ller. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68:673-690. Liu, W. T., T. L. Marsh., H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rDNA. Appl. Environ. Microbiol. 63:4516-4522. Martinez-Murcia A. J., S. G. Acinas, and F. Rodriguez-Valera. 1995. Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol. Ecol. 17:247-256. McCracken, V. J., J. M. Simpson, R. I. Mackie, and H. R. Gaskins. 2001. Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota. J. Nutr. 131:1862-1870. Midtvedt, T. 1986. Intestinal microflora-associated characteristics. Microecol. Ther. 16:121-130. Midtvedt, T., B. Carlstedt-Duke, T. H?verstad, A. C. Midtvedt, K. E. Norm, and H. Saxerholt. 1987. Establishment of a biochemically active intestinal ecosystem in ex-germfree rats. Appl. Environ. Microbiol. 53:2866-2871. Moeseneder, M. M., J. M. Arrieta, G. Muyzer, C. Winter, and G. J. Herndl. 1999. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65:3518-3525. Moore, W. E., and L. V. Holdeman. 1974. The normal flora of 20 Japanese-Hawaiians. Appl. Micorbiol. 27:961-979. Moyer, C. L., J. M. Tiedje, F. C. Dobbs, and D. M. Karl. 1996. A computer simulated restriction fragment length polymorphism analysis of bacterial small subunit RRNA genes: efficacy of selected tetrameric restriction enzyme for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62:2501-2507. Muyzer G. 2000. Genetic fingerprinting of microbial communities-present status and future perspectives. In (Bell et al., Eds) Proceedings of the International Symposium on Microbial Ecology. Nagashima, K., T. Hisada, M. Sato, and J. Mochizuki. 2003. Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces. Appl. Environ. Microbiol. 69:1251-1262. Nei, M. and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press. New York. pp. 245-246. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Ann. Rev. Microbiol. 40:337-365. Pace, N.A., D. A. Stahl, D. J. Lane, G Olsen. 1986. The analysis of natural microbial communities by ribosomal RNA sequences. Adv. Microbiol. Ecol. 9:1-55 Paster, B. J., F E. Dewhirst, S. M. Cooke, V. Fussing, L. K. Poulsen, and J. A. Breznak. 1996. Phylogeny of not-yet-cultured spirochetes from termite guts. Appl. Environ. Microbiol. 62:347-352. Posada, D., K. A. Crandall. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends ecol. and evol. 16:37-45. Pryde, S. E., A. J. Richardson, C. S. Stewart, and H. J. Flint. 1999. Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl. Environ. Microbiol. 65:5372-5377. Randazzo, C. L., S. Torriani, A. D. L. Akkermans, W. M. de Vos, and B. E. Vaughan. 2002. Diversity, Dynamics, and Activity of bacterial communities during production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis. Appl. Environ. Microbiol. 68:1882-1892. Rosenbaum, V. and D. Riesner. 1987. Temperature-gradient gel electrophoresis: Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys. Chem. 26:235-246. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425. Salzman, N. H., H. de Jong, Y. Paterson, H. J. M. Harmsen, G. W. Welling and N. A. Bos. 2002. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Appl. Environ. Microbiol. 148:3651-3660. Savage, D. C. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31: 107-133. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rDNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378. Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin: A software for population genetics data analysis. Ver 2.000. Genetics and Biometry Lab, Dept. of Anthropology, University of Geneva. Available at http://lgb.unige.chlarlequin/ Shannon, C. E., and W. Weaver. 1949. The mathematical theory of communication. Urbana IL: University of Illinois Press. Simpson, E. H. 1949. Measurement of diversity. Nature 163:688. Snel, J., C. C. Hermsen, H. J. Smits, N. A. Bos, W. M. C. Eling, J. J. Cebra, and P. J. Heidt. 1998. Interactions between gut-associated lymphoid tissue and colonization levels of indigenous, segmented, filamentous bacteria in the small intestine of mice. Can. J. Microbiol. 44:1177-1182. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849 Stahl, D. A., D. J. Lane, G. J. Olsen, and N. R. Pace. 1985. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl. Environ. Microbiol. 49:1379-1384. Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321-346. Suau, A., R. Bonnet, M. Sutren, J. J. Godon, G. R. Gibson, M. D. Collins, and J. Dore. 1999. Direct analysis of genes encoding 16S rDNA from complex communitied reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:4799-4807. Swofford, D. L., 1999. PAUP*: phylogenetic analysis using parsimony(*and other method), version 4.0. Sinauer Associates, Sunderland, Massachusetts. S?rheim, R., V. L. Torsvik, and J. Goks?yr. 1989. Phenotypical divergences between populations of soil bacteria isolated on different media. Microb. Ecol. 17:181-192. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460. Tajima, K., R. I. Aminov, T. Nagamine, K. Ogata, M. Nakamura, H. Matsui, and Y. Benno. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29:159-169. Templeton, A. R., K. A. Crandall, and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633. Templeton, A. R., E. Routman, and C. Phillips. 1995. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the Tiger Salamander, Ambystoma tigrinum. Genetics 140:767-782. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity of soil bacteria. Appl. Environ. Microbiol. 56:782-787. Wang, R. F., W. W. Cao, and C. E. Cerniglia. 1996. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl. Environ. Microbiol. 62:1242-1247. Wagner, M., R. Erhart, W. Manz, R. Amann, H. Lemmer, D. Wedi, and K. H. Schleifer. 1994. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:792-800. Weller, R., J. W. Weller, and D. M. Ward. 1991. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57:1146-1151. Whitford, M. F., R. F. Forster, C. E. Beard, J. Gong, and R. M. Teather. 1998. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4:153-163. Wilson, K. H., and R. B. Blitchington. 1996. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62:2273-2278. Wintzingerode, F. V., U. B. G?bel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271. Wintzingerode, F. V., U. B. G?bel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/75368 | - |
| dc.description.abstract | 環境中大部份種類的細菌以目前的培養技術是無法培養或甚至是很難培養的。所以這對於研究微生物的問題上是個很大的瓶頸。目前大部分微生物學家以各種不同種細菌的小段核醣體RNA基因(16S rDNA)，再經過一些分析方法如：ARDRA(RFLP)、DGGE、TGGE、T-RFLP、…等分出不同細菌的遺傳變異作為分類的依據，此方法不需在培養基上培養細菌再做分析，是目前研究微生物相的最好方法。 本研究利用分子生物學的方法來探究野生小家鼠的腸胃道內細菌，分析其組成和變化，期望將來建立一個小家鼠腸胃道細菌相的完整藍圖，對台灣小家鼠族群的分析上及其腸胃道疾病與微生物的相關研究有很大的幫助。因此，首先將野生小家鼠小腸內細菌的16S rDNA進行聚合?連鎖反應(PCR)及細胞轉殖(cloning)，再加以完全定序，以確切地分析細菌相的組成及其親緣關係。發現有六群主要的操作分類單元(OTUs)，其中以OUT A(Mycoplasma sp.)及OUT B (Bacillaceae cereus)為優勢族群而其他族群則非常稀少，進而分析其OTU內單型(haplotype)的變異情形。之後搜尋並下載GenBank上所有哺乳類動物腸胃道細菌的16S rDNA序列，並取其中較完整可用的1114條序列，來進行電腦軟體模擬T-RFLP的操作，找出最合適的PCR引子及限制?，以便將來快速檢測細菌相的組成及變化，發現以55f-985r配對的引子及配合HhaI或RsaI等限制?可產生最多的片段長度(T-RFs)多型性。 | zh_TW |
| dc.description.provenance | Made available in DSpace on 2021-07-01T08:12:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2003 | en |
| dc.description.tableofcontents | Acknowledgments………………………………………………………………………………………………I Abstract ………………………………………………………………………………………………………II Table of Contents……………………………………………………………………………………………III 1. Introduction………………………………………………………………………………………………1 2. Materials and methods …………………………………………………………………………………7 2.1 Sample collections …………………………………………………………………………………7 2.2 Microbial DNA extraction……………………………………………………………………………7 2.3 Amplification of microbial rDNA…………………………………………………………………8 2.4 Cloning and Sequencing………………………………………………………………………………9 2.5 Sequence analysis……………………………………………………………………………………10 2.6 T-RFLP computer simulation…………………………………………………………………………13 3. Results………………………………………………………………………………………………………15 3.1 16S rDNA clones and identification………………………………………………………………15 3.2 Phylogenetic analysis………………………………………………………………………………18 3.3 Genetic variation for OTU A and OTU B…………………………………………………………20 3.4 Haplotype network analysis ………………………………………………………………………21 3.5 T-RFLP simulation……………………………………………………………………………………22 4. Discussion…………………………………………………………………………………………………24 5. References…………………………………………………………………………………………………30 Tables …………………………………………………………………………………………………………36 Figure legends ………………………………………………………………………………………………44 Figures…………………………………………………………………………………………………………47 Appendix A ……………………………………………………………………………………………………62 | |
| dc.language.iso | zh-TW | |
| dc.title | 小家鼠小腸微生物相的遺傳分析 | zh_TW |
| dc.title | Genetic Analysis of the Small Intestine Microflora in Wild House Mouse (Mus musculus castaneus) | en |
| dc.date.schoolyear | 91-2 | |
| dc.description.degree | 碩士 | |
| dc.relation.page | 65 | |
| dc.rights.note | 未授權 | |
| dc.contributor.author-dept | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 動物學研究所 | zh_TW |
| 顯示於系所單位： | 動物學研究所 | |
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