Chan, Wing Hin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 126-143). / Abstracts in English and Chinese. / Acknowledgement --- p.ii / Abstract --- p.iii / 摘要 --- p.vi / Table of Content --- p.viii / List of Figures --- p.xiv / List of Tables --- p.xvi / Abbreviations --- p.xviii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Food and herb authentication --- p.1 / Chapter 1.1.1 --- Background and definition --- p.1 / Chapter 1.1.2 --- Importance of species identification in food and herb authentication --- p.2 / Chapter 1.1.2.1 --- Primary health care --- p.2 / Chapter 1.1.2.2 --- Food and herb safety --- p.3 / Chapter 1.1.2.3 --- Conservation --- p.4 / Chapter 1.1.3 --- Methods for species identification in food and herb authentication --- p.4 / Chapter 1.1.3.1 --- Morphological identification --- p.5 / Chapter 1.1.3.2 --- Chemical analysis --- p.6 / Chapter 1.1.3.3 --- Molecular analysis --- p.9 / Chapter 1.1.4 --- Legislation --- p.11 / Chapter 1.1.4.1 --- Labeling ´ب --- p.11 / Chapter 1.1.4.2 --- Chinese medicine : --- p.12 / Chapter 1.1.4.3 --- Conservation --- p.12 / Chapter 1.2 --- Dongchongxiacao --- p.13 / Chapter 1.2.1 --- Background information of Dongchongxiacao --- p.13 / Chapter 1.2.2 --- Classification of fungal part of Dongchongxiacao --- p.14 / Chapter 1.2.3 --- Dongchongxiacao as a Traditional Chinese Medicine. --- p.15 / Chapter 1.2.4 --- The Dongchongxiacao market --- p.16 / Chapter 1.2.5 --- Adulteration and contamination of Dongchongxiacao --- p.18 / Chapter 1.2.6 --- Authentication of Dongchongxiacao --- p.19 / Chapter 1.2.6.1 --- Morphological identification --- p.19 / Chapter 1.2.6.2 --- Chemical analysis --- p.20 / Chapter 1.2.6.3 --- Molecular analysis --- p.22 / Chapter 1.2.6.3.1 --- "FINS analysis with genomic ITS, nrLSU, EF-lα and rpbl regions for fungal analyses" --- p.22 / Chapter 1.2.6.3.2 --- FINS analysis with mitochondrial CytB and COI regions for caterpillar analyses --- p.24 / Chapter 1.3 --- Abalone --- p.26 / Chapter 1.3.1 --- Background information of abalone --- p.26 / Chapter 1.3.2 --- Abalone as food --- p.27 / Chapter 1.3.3 --- The abalone market --- p.28 / Chapter 1.3.4 --- Adulteration of abalone --- p.31 / Chapter 1.3.5 --- Authentication of abalone --- p.32 / Chapter 1.3.5.1 --- Morphological identification --- p.32 / Chapter 1.3.5.2 --- Chemical analysis --- p.32 / Chapter 1.3.5.3 --- Molecular analysis --- p.33 / Chapter 1.3.5.3.1 --- FINS analysis with mitochondrial COI and 16S rDNA --- p.33 / Chapter 1.3.5.3.2 --- Haliotis-specific detection --- p.34 / Chapter 1.4 --- Aim and Objectives --- p.35 / Chapter Chapter 2 --- Materials and Methods --- p.36 / Chapter 2.1 --- Materials used in this sutdy --- p.36 / Chapter 2.1.1 --- Dongchongxiacao and Cordyceps samples --- p.36 / Chapter 2.1.2 --- Downloaded sequences from NCBI database included in Dongchongxiacao study. --- p.45 / Chapter 2.1.3 --- Abalone and gastropod samples --- p.48 / Chapter 2.1.4 --- Downloaded sequences from NCBI database included in abalone study --- p.54 / Chapter 2.2 --- Reagents and equipments : --- p.56 / Chapter 2.2.1 --- Chemical test on the presence of potassium alum in Dongchongxiacao --- p.56 / Chapter 2.2.2 --- Sample preparation and DNA extraction --- p.57 / Chapter 2.2.3 --- Polymerase Chain Reaction --- p.57 / Chapter 2.2.4 --- Agarose gel electrophoresis and Gene Clean --- p.57 / Chapter 2.2.5 --- Cloning --- p.58 / Chapter 2.2.6 --- Cycle sequencing --- p.58 / Chapter 2.3 --- Experimental procedures --- p.58 / Chapter 2.3.1 --- Morphological observation of Dongchongxiacao and abalone --- p.59 / Chapter 2.3.2 --- Chemical test of potassium in Dongchongxiacao --- p.59 / Chapter 2.3.3 --- Sample preparation and DNA extraction --- p.60 / Chapter 2.3.4 --- Polymerase Chain Reaction --- p.61 / Chapter 2.3.5 --- Agarose gel electrophoresis and Gene Clean --- p.64 / Chapter 2.3.6 --- Cloning --- p.65 / Chapter 2.3.7 --- Cycle sequencing --- p.67 / Chapter 2.3.8 --- Sequence analyses --- p.67 / Chapter 2.3.9 --- Haliotis-specific primer design and PCR test --- p.68 / Chapter Chapter 3 --- Results --- p.71 / Chapter 3.1 --- Dongchongxiacao --- p.71 / Chapter 3.1.1 --- Morphological observations --- p.71 / Chapter 3.1.2 --- Chemical test of potassium alum --- p.77 / Chapter 3.1.3 --- Sequence analyses --- p.79 / Chapter 3.1.4 --- The dendrograms --- p.81 / Chapter 3.2 --- Abalone --- p.91 / Chapter 3.2.1 --- Morphological observations --- p.91 / Chapter 3.2.2 --- Sequence analyses --- p.92 / Chapter 3.2.3 --- The dendrograms --- p.94 / Chapter 3.2.4 --- Haliotis-specific PCR --- p.96 / Chapter Chapter 4 --- Discussion --- p.98 / Chapter 4.1 --- Dongchongxiacao --- p.98 / Chapter 4.1.1 --- Species identification of Dongchongxiacao and related Cordyceps species --- p.98 / Chapter 4.1.1.1 --- Ophiocordyceps sinensis --- p.98 / Chapter 4.1.1.2 --- Cordyceps gunnii --- p.100 / Chapter 4.1.1.3 --- Metacordyceps taii --- p.102 / Chapter 4.1.1.4 --- Cordyceps militaris --- p.103 / Chapter 4.1.2 --- Adulteration of Dongchongxiacao and labeling --- p.104 / Chapter 4.1.3 --- Hosts of Dongchongxiacao fungi and relationship between them --- p.107 / Chapter 4.2 --- Abalone --- p.109 / Chapter 4.2.1 --- Species identification of abalones and other gastropod species by FINS analysis --- p.109 / Chapter 4.2.1.1 --- Haliotis species --- p.109 / Chapter 4.2.1.1.1 --- Haliotis diversicolor --- p.110 / Chapter 4.2.1.1.2 --- Haliotis discus --- p.110 / Chapter 4.2.1.1.3 --- Haliotis asinina --- p.111 / Chapter 4.2.1.1.4 --- Haliotis rufescens --- p.111 / Chapter 4.2.1.1.5 --- Haliotis midae --- p.111 / Chapter 4.2.1.1.6 --- Haliotis madaka --- p.112 / Chapter 4.2.1.1.7 --- Haliotis rubra --- p.113 / Chapter 4.2.1.1.8 --- Haliotis iris --- p.113 / Chapter 4.2.1.1.9 --- Haliotis corrugata --- p.114 / Chapter 4.2.1.2 --- Concholepas concholepas --- p.114 / Chapter 4.2.1.3 --- Hemifusus species --- p.115 / Chapter 4.2.1.4 --- """Dried abalone slice"" samples (D1 to D3) and canned top-shell (E5)" --- p.115 / Chapter 4.2.2 --- Haliotis-speciflc PCR --- p.115 / Chapter 4.2.3 --- Adulteration of abalone and labeling --- p.116 / Chapter 4.3 --- Significance and limitation of molecular approaches in authentication of food and herbs --- p.117 / Chapter 4.3.1 --- FINS analysis --- p.117 / Chapter 4.3.1.1 --- High interspecific variability but low intraspecific variations --- p.118 / Chapter 4.3.1.2 --- Amplification with universal primers --- p.118 / Chapter 4.3.1.3 --- Insufficient DNA sequence available in database --- p.119 / Chapter 4.3.1.4 --- Contamination by foreign DNA and amplification of undesirable DNA in sample mixture --- p.120 / Chapter 4.3.1.5 --- Amplification of degraded DNA --- p.121 / Chapter 4.3.1.6 --- Suggested regions for authentication of Dongchongxiacao and abalone based on FINS analysis results --- p.121 / Chapter 4.3.2 --- PCR with specific primers for targeted amplicons --- p.122 / Chapter 4.3.3 --- Other limitations of molecular approaches in authentication of food and herbs --- p.123 / Chapter 4.4 --- Further investigation --- p.124 / Chapter 4.5 --- Conclusion --- p.124 / References : --- p.126 / Chapter Appendix 1 --- Sequence alignment of 16S rDNA gene sequences of abalone for Haliotis-specific primer design --- p.144 / Chapter Appendix 2 --- Accession numbers of sequences of Dongchongxiacao and Cordyceps samples in this study --- p.149 / Chapter Appendix 3 --- Search results of CytB sequences of caterpillar host of Cordyceps samples based on BLAST search results from GenBank --- p.150 / Chapter Appendix 4 --- Search results of COI sequences of caterpillar host of Cordyceps samples based on BLAST search results from GenBank --- p.151 / Chapter Appendix 5 --- Search results of COI sequences of caterpillar host of Cordyceps samples based on BLAST search results from GenBank --- p.152 / Chapter Appendix 6 --- Sequence alignment of ITS sequences of Cordyceps samples and related sequences --- p.153 / Chapter Appendix 7 --- Sequence alignment of nrLSU sequences of Cordyceps samples and related sequences --- p.161 / Chapter Appendix 8 --- Sequence alignment of EF-lα sequences of Cordyceps samples and related sequences --- p.168 / Chapter Appendix 9 --- Sequence alignment of rpbl sequences of Cordyceps samples and related sequences --- p.173 / Chapter Appendix 10 --- "Sequence alignment of combined dataset of three regions (nrLSU, EF-lα and rpbl) of Cordyceps samples and related sequences" --- p.179 / Chapter Appendix 11 --- Sequences alignment of CytB sequences of caterpillar host of Cordyceps samples and related sequences --- p.188 / Chapter Appendix 12 --- Sequence alignment of COI sequences of caterpillar host of Cordyceps samples and related sequences --- p.191 / Chapter Appendix 13 --- Sequence alignment of COI sequences of Cordyceps samples D12-2 and D14 and related sequences --- p.195 / Chapter Appendix 14 --- Sequence distance matrix of ITS sequences of Cordyceps samples and related samples based on K2P algorithm --- p.196 / Chapter Appendix 15 --- Sequence distance matrix of nrLSU sequences of Cordyceps samples and related samples based on K2P algorithm --- p.203 / Chapter Appendix 16 --- Sequence distance matrix of EF-lα sequences of Cordyceps samples and related samples based on K2P algorithm --- p.208 / Chapter Appendix 17 --- Sequence distance matrix of rpbl sequences of Cordyceps samples and related samples based on K2P algorithm --- p.213 / Chapter Appendix 18 --- "Sequence distance matrix of combined dataset of three regions (nrLSU, EF-lα and rpbl) sequences of Cordyceps samples and related samples based on K2P algorithm" --- p.217 / Chapter Appendix 19 --- Sequence distance matrix of CytB sequences of caterpillar host of Cordyceps samples and related samples based on K2P algorithm --- p.219 / Chapter Appendix 20 --- Sequence distance matrix of COI sequences of caterpillar host of Cordyceps samples and related samples based on K2P algorithm --- p.223 / Chapter Appendix 21 --- Sequence alignment of chloroplast trnH-psbA sequences of Cordyceps sample D12-2 and related sequences --- p.226 / Chapter Appendix 22 --- Accession numbers of sequences of abalone and gastropod samples in this study --- p.227 / Chapter Appendix 23 --- Search results of 16S rDNA sequences of the abalone and gastropod samples based on BLAST search results from GenBank --- p.228 / Chapter Appendix 24 --- Search results of COI sequences of the abalone and gastropod samples based on BLAST search results from GenBank --- p.229 / Chapter Appendix 25 --- Search results of COI sequences of the abalone and gastropod samples based on BOLD-IDS --- p.230 / Chapter Appendix 26 --- Sequence alignment of 16S sequences of abalone samples and related sequences --- p.231 / Chapter Appendix 27 --- Sequence alignment of COI sequences of abalone samples and related sequences --- p.234 / Chapter Appendix 28 --- Sequence alignment of COI sequences of abalone product sample D2 and related sequences --- p.238 / Chapter Appendix 29 --- Sequence distance matrix of 16S sequences of abalone samples and related samples based on K2P algorithm --- p.239 / Chapter Appendix 30 --- Sequence distance matrix of COI sequences of abalone samples and related samples based on K2P algorithm --- p.243

Yip Pui Ying. / Thesis submitted in: November 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 147-184). / Abstracts in English and Chinese. / Abstract --- p.i / 摘要 --- p.iii / Acknowledgment --- p.v / Abbreviations --- p.vii / Table of contents --- p.viii / List of Figures --- p.xii / List of Tables --- p.xvii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1. --- The importance of characterization of Chinese medicinal materials and the development of Chinese medicine in Hong Kong --- p.1 / Chapter 1.2. --- Methods for characterization of Chinese medicinal materials --- p.5 / Chapter 1.3. --- Molecular characterization of Chinese medicinal materials --- p.8 / Chapter 1.3.1. --- DNA sequencing --- p.9 / Chapter 1.3.2. --- DNA fingerprinting --- p.14 / Chapter 1.3.3. --- Nucleic acid hybridization --- p.19 / Chapter 1.4. --- Objectives --- p.20 / Chapter Chapter 2 --- Characterization of Plant and Fungal Materials by rDNA ITS Sequence Analysis --- p.22 / Chapter 2.1. --- Introduction --- p.22 / Chapter 2.2. --- Materials and Methods --- p.22 / Chapter 2.2.1. --- Chinese medicinal materials used in this study --- p.22 / Chapter 2.2.1.1. --- Plants and fungi for interspecific ITS study --- p.22 / Chapter 2.2.1.2. --- Plant for intraspecific ITS study and locality study --- p.33 / Chapter 2.2.2. --- Extraction of total DNA --- p.35 / Chapter 2.2.3. --- PCR amplification of ITS1 and ITS2 regions of rRNA gene --- p.35 / Chapter 2.2.4. --- Purification of PCR products --- p.38 / Chapter 2.2.5. --- Cloning using pCR-Script´ёØ Amp SK(+) Cloning Kit --- p.38 / Chapter 2.2.5.1. --- Polishing --- p.38 / Chapter 2.2.5.2. --- Ligation of inserts into pCR-Script´ёØ Amp SK(+) cloning vector --- p.38 / Chapter 2.2.5.3. --- Transformation --- p.40 / Chapter 2.2.5.4. --- PCR screening of white colonies --- p.40 / Chapter 2.2.5.5. --- Purification of PCR screening products --- p.41 / Chapter 2.2.6. --- Sequencing of ITS regions --- p.41 / Chapter 2.2.6.1. --- Cycle sequencing reaction --- p.41 / Chapter 2.2.6.2. --- Purification of sequencing extension products --- p.41 / Chapter 2.2.6.3. --- Electrophoresis by genetic analyzer --- p.42 / Chapter 2.2.7. --- Sequence analysis and alignment --- p.42 / Chapter 2.3. --- Results --- p.42 / Chapter 2.3.1. --- Extraction of total DNA --- p.42 / Chapter 2.3.2. --- PCR amplification of ITS1 and ITS2 regions of rRNA gene --- p.44 / Chapter 2.3.2.1. --- Interspecific ITS study --- p.44 / Chapter 2.3.2.2. --- Intraspecific ITS study --- p.46 / Chapter 2.3.3. --- Sequence analysis and alignment --- p.47 / Chapter 2.3.3.1. --- Interspecific ITS study --- p.47 / Chapter 2.3.3.2. --- Intraspecific ITS study --- p.56 / Chapter 2.4. --- Discussions --- p.60 / Chapter 2.4.1. --- rDNA regions used for studying Chinese medicinal materials --- p.60 / Chapter 2.4.2. --- The results agreed with previously published works --- p.60 / Chapter 2.4.3. --- Explanation of interspecific results within the Ganoderma genus --- p.60 / Chapter 2.4.4. --- Implications from interspecific comparisons --- p.60 / Chapter 2.4.5. --- Implications from intraspecific comparisons --- p.61 / Chapter Chapter 3 --- .Characterization of Astragalus membranaceus by DNA Fingerprinting / Chapter 3.1 --- Introduction --- p.62 / Chapter 3.2 --- Materials and Methods --- p.62 / Chapter 3.2.1 --- Extraction of total DNA --- p.62 / Chapter 3.2.2 --- Generation and detection of DNA fingerprints by AP-PCR --- p.63 / Chapter 3.2.3 --- Analysis of DNA fingerprints --- p.63 / Chapter 3.3 --- Results --- p.63 / Chapter 3.3.1 --- Generation of DNA fingerprints by AP-PCR --- p.63 / Chapter 3.3.2 --- Fingerprint analysis --- p.69 / Chapter 3.4 --- Discussion --- p.85 / Chapter 3.4.1 --- RP-PCR has been used on Chinese medicinal materials --- p.85 / Chapter 3.4.2 --- AP-PCR used instead of RAPD --- p.85 / Chapter 3.4.3 --- Reproducibility and amount of bands --- p.86 / Chapter 3.4.4 --- Alternatives of electrophoresis process --- p.88 / Chapter 3.4.5 --- Explanation of results --- p.88 / Chapter 3.4.6 --- Distinguishing Neimengu and Shanxi samples --- p.89 / Chapter 3.4.7 --- Further studies --- p.90 / Chapter Chapter 4 --- Characterization of Plant and Fungal Materials by DNA-DNA Hybridization on Microarrays --- p.91 / Chapter 4.1 --- Introduction --- p.91 / Chapter 4.2 --- Materials and Methods --- p.92 / Chapter 4.2.1 --- Samples for microarray study --- p.92 / Chapter 4.2.2 --- Extraction of total DNA --- p.95 / Chapter 4.2.3 --- Amplification and sequencing of ITS 1 region of rRNA gene --- p.95 / Chapter 4.2.4 --- Preparation of labeled probe --- p.95 / Chapter 4.2.5 --- Amplification of ITS1 fragments --- p.97 / Chapter 4.2.6 --- Preparation of slides --- p.103 / Chapter 4.2.7 --- Hybridization and washing --- p.104 / Chapter 4.2.8 --- Scanning and data analysis --- p.105 / Chapter 4.3 --- Results --- p.105 / Chapter 4.3.1 --- DNA extraction --- p.105 / Chapter 4.3.2 --- Amplification and sequencing of ITS1 region of rRNA gene --- p.107 / Chapter 4.3.3 --- Preparation of labeled probe and amplification of ITS1 fragments… --- p.112 / Chapter 4.3.4 --- Preparation of slides --- p.112 / Chapter 4.3.5 --- Scanning and data analysis --- p.116 / Chapter 4.4 --- Discussion --- p.134 / Chapter 4.4.1 --- Implications --- p.134 / Chapter 4.4.2 --- Applying the findings --- p.134 / Chapter 4.4.3 --- Ways to maximize specificity --- p.137 / Chapter 4.4.4 --- Optimisation --- p.138 / Chapter 4.4.5 --- Microarray may be more advantageous over sequencing --- p.138 / Chapter Chapter Five --- General Discussion and Summary --- p.140 / Chapter 5.1. --- Objectives of this study --- p.140 / Chapter 5.2. --- rDNA ITS sequencing --- p.140 / Chapter 5.2.1. --- Description of the approach and summary of the results --- p.140 / Chapter 5.2.2. --- Implications from the results --- p.140 / Chapter 5.2.3. --- Advantages and limitations of DNA sequencing --- p.141 / Chapter 5.3. --- AP-PCR fingerprinting --- p.141 / Chapter 5.3.1. --- Description of the approach and summary of the results --- p.141 / Chapter 5.3.2. --- Advantages and limitations of DNA fingerprinting --- p.142 / Chapter 5.4. --- DNA-DNA hybridization on microarrays --- p.143 / Chapter 5.4.1. --- Description of the approach and summary of the results --- p.143 / Chapter 5.4.2. --- Implications from the results --- p.143 / Chapter 5.4.3. --- Advantages and limitations of DNA hybridization on microarrays. --- p.144 / Chapter 5.5. --- Overall summary --- p.144 / Chapter 5.6. --- Future studies --- p.146 / References --- p.147 / Appendix --- p.185