Zhang Junjun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 147-160). / Abstracts in English and Chinese. / Thesis Committee --- p.i / Statement from Author --- p.ii / Acknowledgements --- p.iii / Abstract --- p.v / 摘要 --- p.vii / Table of Contents --- p.ix / List of Tables --- p.xiv / List of Figures --- p.xvi / List of Abbreviations --- p.xviii / Chapter Chapter 1 --- General Introduction and Literature Review --- p.1 / Chapter 1.1 --- General Introduction --- p.1 / Chapter 1.2 --- Literature Review --- p.2 / Chapter 1.2.1 --- Rice as a Model Monocot Cereal --- p.2 / Chapter 1.2.1.1 --- Genome Size --- p.3 / Chapter 1.2.1.2 --- Synteny --- p.3 / Chapter 1.2.1.3 --- Well-mapped Genome --- p.4 / Chapter 1.2.1.4 --- Amenable to Transformation --- p.4 / Chapter 1.2.2 --- Rice Genome Sequencing --- p.4 / Chapter 1.2.3 --- Rice Functional Genomics --- p.6 / Chapter 1.2.3.1 --- International Collaboration on Rice Functional Genomics --- p.6 / Chapter 1.2.3.2 --- Recent Progress on Rice Functional Genomics in China --- p.7 / Chapter 1.2.4 --- Large-scale Expressed Sequenced Tag (EST) Analysis --- p.8 / Chapter 1.2.4.1 --- Introduction --- p.8 / Chapter 1.2.4.2 --- Large-scale EST Analysis vs. SAGE and MPSS: Advantages and Shortcomings --- p.12 / Chapter 1.2.4.3 --- Large-scale Rice EST analysis --- p.14 / Chapter 1.2.4.4 --- Seed Specific Large-scale EST Analysis --- p.16 / Chapter 1.2.4.5 --- Bioinformatics Tools Involved --- p.17 / Chapter 1.2.5 --- Profiling Gene Expression using cDNA Microarray --- p.20 / Chapter 1.2.5.1 --- Introduction --- p.20 / Chapter 1.2.5.2 --- Advantages of cDNA Microarray in Gene Expression Profiling --- p.22 / Chapter 1.2.5.3 --- Profiling Gene Expression by cDNA Microarrays --- p.24 / Chapter 1.2.5.4 --- Profiling Seed-specific Gene Expression --- p.26 / Chapter 1.2.6 --- Overview of Current Information on the Biosynthesis and Gene Regulation of Major Components during Rice Seed Formation --- p.30 / Chapter 1.2.6.1 --- Starch --- p.30 / Chapter 1.2.6.2 --- Storage Proteins --- p.38 / Chapter 1.2.6.3 --- Lipids --- p.42 / Chapter Chapter 2 --- Materials and Methods --- p.44 / Chapter 2.1 --- Materials --- p.44 / Chapter 2.1.1 --- Chemicals --- p.44 / Chapter 2.1.2 --- Facilities and Instruments --- p.45 / Chapter 2.1.3 --- Commercial Kits --- p.46 / Chapter 2.1.4 --- Oligonucleotides --- p.47 / Chapter 2.1.5 --- Plant Materials --- p.50 / Chapter 2.1.6 --- Bacterial Strains --- p.52 / Chapter 2.2 --- Methods --- p.52 / Chapter 2.2.1 --- mRNA Isolation --- p.52 / Chapter 2.2.2 --- Construction of cDNA Library --- p.53 / Chapter 2.2.2.1 --- Construction of cDNA Library in Phage --- p.53 / Chapter 2.2.2.2 --- Construction of cDNA Library in E.coli --- p.56 / Chapter 2.2.3 --- Screening of cDNA Library --- p.62 / Chapter 2.2.3.1 --- In situ Hybridization --- p.62 / Chapter 2.2.3.2 --- Probe Synthesis --- p.63 / Chapter 2.2.3.3 --- Hybridization and Detection --- p.64 / Chapter 2.2.4 --- Single-pass Sequencing of cDNAs --- p.65 / Chapter 2.2.5 --- Sequence Analysis --- p.67 / Chapter 2.2.6 --- BLAST Search --- p.71 / Chapter 2.2.7 --- Contig Analysis --- p.71 / Chapter 2.2.8 --- Database Management --- p.72 / Chapter 2.2.9 --- Selection Criteria for ESTs in Different Pathways --- p.72 / Chapter 2.2.10 --- Construction of Super Hybrid Rice Seed cDNA Microarray --- p.75 / Chapter 2.2.11 --- "Probe Synthesis, Microarray Hybridization and Detection" --- p.75 / Chapter 2.2.12 --- Quality Test of External Control --- p.78 / Chapter 2.2.13 --- Scanning of Microarray --- p.79 / Chapter 2.2.14 --- Analysis of Microarray Data --- p.79 / Chapter 2.2.15 --- Normalization --- p.79 / Chapter 2.2.16 --- Northern Blot Analysis --- p.80 / Chapter Chapter 3 --- Results and Discussion --- p.82 / Chapter 3.1 --- cDNA Libraries --- p.82 / Chapter 3.1.1 --- cDNA Library in Phage --- p.82 / Chapter 3.1.2 --- cDNA Library in E.coli --- p.84 / Chapter 3.2 --- Statistic Data of Screening and Single-pass Sequencing --- p.87 / Chapter 3.3 --- Genes Expressing in Developing Rice Seeds --- p.89 / Chapter 3.4 --- Novel ESTs in the Seed EST Set --- p.94 / Chapter 3.5 --- Unique Genes in the EST Set from the Phage cDNA Library --- p.94 / Chapter 3.6 --- Mapping ESTs onto Rice Genome --- p.95 / Chapter 3.7 --- The Most Abundant Transcripts Reflected by EST Redundancy --- p.98 / Chapter 3.8 --- ESTs and Representive Genes in Different Pathways --- p.102 / Chapter 3.9 --- ESTs Involved in Carbon Flows --- p.106 / Chapter 3.10 --- Microarray Configuration and Contents --- p.109 / Chapter 3.11 --- Quantification of Total RNA from Seeds at 5 Developing Stages --- p.110 / Chapter 3.12 --- Quality Test of External Control --- p.111 / Chapter 3.13 --- Scanning of Array Hybridization --- p.113 / Chapter 3.14 --- Reproducibility of Technical Duplicates --- p.116 / Chapter 3.15 --- Summary of Gene Expression Profiles in Developing Super Hybrid Rice Seeds --- p.117 / Chapter 3.16 --- Expression Profiles of Major Storage Compounds in Rice Seeds --- p.119 / Chapter 3.16.1 --- Expression profiles of storage protein genes --- p.119 / Chapter 3.16.2 --- Expression Profiles of Starch Synthesis Related Genes --- p.122 / Chapter 3.16.3 --- Expression Profiles of Lipid Synthesis Related Genes --- p.124 / Chapter 3.16.4 --- General Expression Patterns of Major Storage Compounds --- p.126 / Chapter 3.18 --- General Discussion --- p.131 / Chapter 3.18.1 --- Cautions when Interpreting the EST Data --- p.131 / Chapter 3.18.2 --- Comparison of EST Data Sets of Developing Seeds between Arabidopsis and Rice --- p.131 / Chapter 3.18.3 --- Comparison of cDNA Library Construction by Two Methods --- p.135 / Chapter 3.18.4 --- Comparison of Different Normalization Methods --- p.138 / Chapter 3.18.5 --- Comparison between Microarray and Northern Data --- p.140 / Chapter Chapter 4 --- Conclusion --- p.142 / Chapter Chapter 5 --- Future Perspectives --- p.145 / Reference Lists --- p.147
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_325183 |
| Date | January 2005 |
| Contributors | Zhang, Junjun., Chinese University of Hong Kong Graduate School. Division of Biology. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | print, xvii, 160 leaves : ill. ; 30 cm. |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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