Ha Wai-Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 166-180). / Abstracts in English and Chinese. / Acknowledgements --- p.ii / Abstract --- p.iii / Abbreviations --- p.vi / Table of Contents --- p.vii / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter 1.1 --- "Hstory, cultivation and trade" --- p.2 / Chapter 1.2 --- Botany --- p.4 / Chapter 1.3 --- Chemical Constituents and Pharmacological effects --- p.8 / Chapter 1.4 --- Authentication of Chinese herbal materials --- p.13 / Chapter 1.4.1 --- Morphological marker --- p.15 / Chapter 1.4.2 --- Histological marker --- p.18 / Chapter 1.4.3 --- Chemical marker --- p.20 / Chapter 1.4.4 --- Molecular markers --- p.24 / Chapter 1.4.4.1 --- Protein marker --- p.24 / Chapter 1.4.4.2 --- DNA-based markers --- p.26 / Chapter 1.4.4.2.1 --- PCR-based markers --- p.27 / Chapter 1.4.4.2.1.1 --- Random-primed PCR --- p.28 / Chapter 1.4.4.2.1.2 --- Simple Sequence Repeats (SSR) --- p.30 / Chapter 1.4.4.2.1.3 --- Polymerase Chain Reaction Fragment Length Polymorphism (PCR-RFLP) --- p.31 / Chapter 1.4.4.2.2 --- Hybridization-based markers --- p.33 / Chapter 1.4.4.2.3 --- Sequencing-based markers --- p.35 / Chapter 1.5 --- Objectives and Strategies of the studies --- p.39 / Chapter Chapter 2 --- General Materials and Methods --- p.40 / Chapter 2.1 --- Reagents and Buffers --- p.41 / Chapter 2.1.1 --- Media for bacterial culture --- p.41 / Chapter 2.1.2 --- Reagents for preparation of competent cells --- p.42 / Chapter 2.1.3 --- Reagents for plasmid DNA preparation --- p.42 / Chapter 2.1.4 --- Reagents for agarose gel electrophoresis --- p.43 / Chapter 2.1.5 --- Reagents for polyacrylamide gel electrophoresis --- p.43 / Chapter 2.1.6 --- Reagents for Southern hybridization --- p.44 / Chapter 2.2 --- Agarose Gel electrophoresis of DNA --- p.46 / Chapter 2.3 --- Purification of PCR products --- p.46 / Chapter 2.3.1 --- From agarose gel using Geneclean® II kit --- p.46 / Chapter 2.3.2 --- Using Microspin´ёØ Column --- p.47 / Chapter 2.4 --- End modification of PCR amplified DNA --- p.47 / Chapter 2.5 --- Preparation of Escherichia coli Competent Cells --- p.48 / Chapter 2.6 --- "Ligation and Transformation of E, coli" --- p.49 / Chapter 2.7 --- Plasmid Preparation --- p.50 / Chapter 2.7.1 --- Minipreparation of plasmid DNA --- p.50 / Chapter 2.7.2 --- Preparation of plasmid DNA using Wizard® Plus SV Minipreps DNA Purification Kit (Promega) --- p.50 / Chapter 2.8 --- Screening for the Presence of insert in plasmid --- p.51 / Chapter 2.8.1 --- Rapid alkaline lysis --- p.51 / Chapter 2.8.2 --- PCR screening --- p.52 / Chapter 2.8.3 --- Restriction digestion of plasmid DNA --- p.53 / Chapter 2.9 --- DNA sequencing --- p.53 / Chapter 2.9.1 --- Plasmid sequencing using T7 Sequencing Kit --- p.53 / Chapter 2.9.2 --- Cycle Sequencing from PCR products or plasmid --- p.54 / Chapter 2.10 --- DNA Sequencing electrophoresis --- p.55 / Chapter 2.10.1 --- Preparation of 6 % polyacrylamide gel solution --- p.55 / Chapter 2.10.2 --- Gel casting --- p.55 / Chapter 2.10.3 --- Electrophoresis of Sequencing Gel --- p.56 / Chapter 2.10.4 --- Autoradiography --- p.57 / Chapter 2.11 --- DNA elution from dried sequencing gel --- p.57 / Chapter 2.12 --- Southern blot analysis --- p.58 / Chapter 2.12.1 --- Restriction digestion of genomic DNA --- p.58 / Chapter 2.12.2 --- Purification of digested DNA and agarose gel electrophoresis --- p.58 / Chapter 2.12.3 --- Capillary transfer of DNA to a Hybond´ёØ N+ nylon membrane --- p.59 / Chapter 2.12.4 --- DNA radiolabeling by nick translation --- p.60 / Chapter 2.12.5 --- Purificaiton of radiolabeled probe by NICK® Spin Column --- p.60 / Chapter 2.12.6 --- Hybridization of DNA --- p.61 / Chapter Chapter 3 --- Plant DNA extraction --- p.62 / Chapter 3.1 --- Introduction --- p.63 / Chapter 3.2 --- Reagents and buffer for total DNA extraction --- p.66 / Chapter 3.3 --- Extraction methods --- p.70 / Chapter 3.3.1 --- Sample preparation --- p.70 / Chapter 3.3.2 --- CTAB extraction method --- p.70 / Chapter 3.3.3 --- Potassium acetate/ SDS extraction method --- p.71 / Chapter 3.3.4 --- GIBRO Plant DNAzol® reagent for genomic DNA isolation --- p.72 / Chapter 3.4 --- Qualitative and quantitative analysis of DNA --- p.74 / Chapter 3.5 --- Results --- p.75 / Chapter 3.6 --- Discussion --- p.78 / Chapter Chapter 4 --- Amplified Fragment Length Polymorphism (AFLP) analysis of P. ginseng and P. quinquefolius --- p.81 / Chapter 4.1 --- Introduction --- p.82 / Chapter 4.2 --- Materials and methods --- p.88 / Chapter 4.2.1 --- Plant materials --- p.88 / Chapter 4.2.2 --- Choice of Primers and radiolabeling --- p.89 / Chapter 4.2.3 --- AFLP assay --- p.90 / Chapter 4.2.4 --- Electrophoresis of AFLP fingerprint --- p.91 / Chapter 4.2.5 --- Similarity Index (S.I.) analysis of AFLP profile --- p.91 / Chapter 4.2.6 --- Re-amplification of polymorphic DNA fragments isolated from dried sequencing gel --- p.92 / Chapter 4.2.7 --- Cloning and Sequencing of the AFLP fragments --- p.93 / Chapter 4.2.8 --- Conversion of AFLP marker into Directed Amplification of Minisatellite-region DNA polymorphism (DAMD) marker --- p.93 / Chapter 4.3 --- Results --- p.95 / Chapter 4.4 --- Discussion --- p.102 / Chapter Chapter 5 --- Direct Amplification of Length Polymorphisms (DALP) analysis of P. ginseng and P. quinquefolius --- p.107 / Chapter 5.1 --- Introduction --- p.108 / Chapter 5.2 --- Materials and methods --- p.112 / Chapter 5.2.1 --- Plant materials --- p.112 / Chapter 5.2.2 --- Choice of Primers --- p.113 / Chapter 5.2.3 --- Alternative labelled Amplification reaction --- p.114 / Chapter 5.2.4 --- Electrophoresis of the multi-locus amplification products --- p.114 / Chapter 5.2.5 --- Isolation and Re-amplification of polymorphic DALP fragments from dried sequencing gel --- p.115 / Chapter 5.2.6 --- Cloning and Sequencing --- p.115 / Chapter 5.2.7 --- Conversion of DALP marker to Sequence Tagged Site (STS) marker --- p.116 / Chapter 5.3 --- Results --- p.117 / Chapter 5.4 --- Discussion --- p.135 / Chapter Chapter 6 --- Sequence-characterized amplified region (SCAR): the sequel of random amplified polymorphic DNA (RAPD) --- p.137 / Chapter 6.1 --- Introduction --- p.138 / Chapter 6.2 --- Materials and methods --- p.140 / Chapter 6.2.1 --- Plant materials --- p.140 / Chapter 6.2.2 --- PCR reaction --- p.141 / Chapter 6.2.3 --- Cloning and sequencing --- p.143 / Chapter 6.3 --- Results --- p.144 / Chapter 6.4 --- Discussion --- p.157 / Chapter Chapter 7 --- Outlook --- p.159 / Chapter 7.1 --- Molecular authentication of Chinese medicinal materials --- p.160 / Chapter 7.2 --- Development of molecular markers for Ginseng --- p.161 / Appendix I --- p.164 / Appendix II --- p.165 / References --- p.166

by Ngan Fai Ngor Karenda. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 128-134). / Acknowledgements --- p.i / Abstract --- p.ii / Table of Contents --- p.iii / Abbreviations --- p.viii / Chapter Chapter 1 --- Authentication of Chinese Medicinal Herbs / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Traditional Identification of Chinese Herbs / Chapter 1.2.1 --- Morphology --- p.3 / Chapter 1.2.2 --- Histology --- p.4 / Chapter 1.2.3 --- Chemical Analysis --- p.4 / Chapter 1.2.4 --- Proteins and Isozymes --- p.6 / Chapter 1.3 --- Molecular Technology in Authentication / Chapter 1.3.1 --- Restriction Fragment Length Polymorphism (RFLP) --- p.6 / Chapter 1.3.2 --- Polymerase Chain Reactions (PCRs) / Chapter 1.3.2.1 --- Random-Primed PCRs --- p.8 / Chapter 1.3.2.2 --- Simple Sequence Repeats --- p.10 / Chapter 1.3.2.3 --- Amplified Fragment Length Polymorphism (AFLP) --- p.11 / Chapter 1.4 --- Objectives and Strategies of the Study --- p.13 / Chapter Chapter 2 --- Materials and Methods / Chapter 2.1 --- Reagents and Buffers / Chapter 2.1.1 --- Buffers for Total DNA Extraction --- p.15 / Chapter 2.1.2 --- Reagents for Agarose Gel Electrophoresis --- p.16 / Chapter 2.1.3 --- Reagents for Polyacrylamide Gel Electrophoresis --- p.17 / Chapter 2.1.4 --- Reagents for Plasmid and Single-Stranded DNA Preparation --- p.17 / Chapter 2.1.5 --- Media for Bacterial Culture --- p.19 / Chapter 2.1.6 --- Reagents for Preparation of Competent Cells --- p.20 / Chapter 2.2 --- DNA Isolation / Chapter 2.2.1 --- Sample Preparation --- p.21 / Chapter 2.2.2 --- Cetyl triethylammonium bromide (CTAB) Extraction --- p.21 / Chapter 2.2.3 --- Cesium Chloride Gradient Ultracentrifugation --- p.21 / Chapter 2.3 --- Phenol/Chloroform Extraction --- p.22 / Chapter 2.4 --- Ethanol Precipitation --- p.23 / Chapter 2.5 --- DNA Concentration/Purity Estimation --- p.23 / Chapter 2.6 --- Random-Primed Polymerase Chain Reactions / Chapter 2.6.1 --- Random Amplified Polymorphic DNA (RAPD) --- p.24 / Chapter 2.6.2 --- Arbitarily-Primed Polymerase Chain Reaction (AP-PCR) --- p.24 / Chapter 2.7 --- rDNA Amplification --- p.24 / Chapter 2.8 --- Agarose Gel Electrophoresis of DNA --- p.25 / Chapter 2.9 --- Purification of rDNA / Chapter 2.9.1 --- from Agarose Gel using Geneclean II Kit (Bio 101 Inc.) --- p.25 / Chapter 2.9.2 --- using Microspin´ёØ Columns --- p.26 / Chapter 2.10 --- Preparation of Escherichia coli Competent Cells --- p.26 / Chapter 2.11 --- Ligation and Transformation of Escherichia coli --- p.27 / Chapter 2.12 --- Isolation of Plasmid DNA --- p.27 / Chapter 2.13 --- Screening of Plasmid DNA by Restriction Digestion --- p.28 / Chapter 2.14 --- Isolation of Plasmid DNA / Chapter 2.14.1 --- Minipreparation of Plasmid using Magic´ёØ Miniprep DNA Purification Kit from Promega --- p.28 / Chapter 2.14.2 --- Megapreparation of Plasmid using Qiagen-tip100 --- p.28 / Chapter 2.15 --- Single-Stranded DNA Preparation / Chapter 2.15.1 --- Transfection --- p.29 / Chapter 2.15.2 --- Single-Stranded DNA Isolation --- p.29 / Chapter 2.16 --- DNA Sequencing / Chapter 2.16.1 --- Plasmid Sequencing using T7 Sequencing Kit --- p.30 / Chapter 2.16.2 --- Cycle Sequencing from PCR Products --- p.30 / Chapter 2.16.3 --- Cycle Sequencing from PCR Products or Plasmid --- p.31 / Chapter 2.16.4 --- DNA Sequencing Electrophoresis --- p.31 / Chapter Chapter 3 --- Studies of Panax Species by Random-Primed PCRs / Chapter 3.1 --- Introduction --- p.34 / Chapter 3.2 --- Materials and Methods / Chapter 3.2.1 --- Plant Materials --- p.39 / Chapter 3.2.2 --- DNA Extraction and Random-Primed PCRs --- p.39 / Chapter 3.2.3 --- Data Analysis --- p.39 / Chapter 3.3 --- Results and Discussion / Chapter 3.3.1 --- DNA Isolation --- p.40 / Chapter 3.3.2 --- DNA Fingerprinting --- p.41 / Chapter 3.3.3 --- Relationship between the Six Panax Species --- p.45 / Chapter Chapter 4 --- Studies of Acorus by Random-Primed PCRs / Chapter 4.1 --- Introduction --- p.48 / Chapter 4.2 --- Materials and Methods / Chapter 4.2.1 --- Plant Materials --- p.49 / Chapter 4.2.2 --- DNA Extraction and Random-Primed PCRs --- p.50 / Chapter 4.3 --- Results and Discussion / Chapter 4.3.1 --- Acorus DNA --- p.50 / Chapter 4.3.2 --- Reproducibility of Random-Primed PCRs --- p.51 / Chapter 4.3.3 --- DNA Fingerprinting --- p.53 / Chapter Chapter 5 --- Studies of Epimedium by Random-Primed PCRs / Chapter 5.1 --- Introduction --- p.70 / Chapter 5.2 --- Materials and Methods / Chapter 5.2.1 --- Plant Materials --- p.71 / Chapter 5.2.2 --- DNA Extraction and Random-Primed PCRs --- p.71 / Chapter 5.3 --- Results and Discussion / Chapter 5.3.1 --- DNA Extraction --- p.71 / Chapter 5.3.2 --- DNA Fingerprinting --- p.72 / Chapter Chapter 6 --- Application of AP-PCR in Commercial Ginseng Products / Chapter 6.1 --- Introduction --- p.90 / Chapter 6.2 --- Materials and Methods / Chapter 6.2.1 --- Materials --- p.91 / Chapter 6.2.2 --- DNA Extraction and Random-Primed PCRs --- p.91 / Chapter 6.2.3. --- Data Analysis --- p.91 / Chapter 6.3 --- Results and Discussion / Chapter 6.3.1 --- DNA Isolation --- p.92 / Chapter 6.3.2 --- AP-PCR Analysis --- p.93 / Chapter Chapter 7 --- Ribosomal DNA as a Marker in Authentication of Panax Species / Chapter 7.1 --- Introduction --- p.99 / Chapter 7.2 --- Materials and Methods / Chapter 7.2.1 --- Plant Materials --- p.100 / Chapter 7.2.2 --- DNA Extraction and rDNA Amplification --- p.101 / Chapter 7.2.3 --- rDNA Sequencing --- p.101 / Chapter 7.2.4 --- Generation of Restriction Fragment Length Polymorphisms / Chapter 7.2.4.1 --- Restriction Digestion of rDNA Fragment --- p.102 / Chapter 7.2.4.2 --- Polyacrylamide Gel Electrophoresis (PAGE) --- p.103 / Chapter 7.2.4.3 --- Silver Staining for Nucleic Acids --- p.103 / Chapter 7.2.5 --- Data Analysis --- p.104 / Chapter 7.3 --- Results and Discussion / Chapter 7.3.1 --- rDNA Amplification and Plasmid Isolation --- p.104 / Chapter 7.3.2 --- rDNA Sequencing / Chapter 7.3.2.1 --- Sequence Comparison between the Six Panax species and the Two Adulterants --- p.107 / Chapter 7.3.3 --- Restriction Fragment Length Polymorphisms / Chapter 7.3.3.1 --- Restriction Profiles between Ginsengs and their Adulterants --- p.113 / Chapter 7.3.3.2 --- Restrciton Profiles of Ginsengs from Different Sources --- p.118 / Chapter 7.3.4 --- Panax Phylogeny --- p.121 / Chapter Chapter 8 --- General Discussion / Chapter 8.1 --- Advantages of Random-Primed PCRs --- p.124 / Chapter 8.2 --- Weaknesses of the Random-Primed PCRs --- p.125 / Chapter 8.3 --- Molecular Markers for Phylogenetic Studies --- p.126 / Chapter 8.4 --- Specific PCR-RFLP Patterns in Authentication --- p.126 / Chapter 8.5 --- Conclusions --- p.127 / References --- p.128 / Appendix --- p.135

Lam, Hilary. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 182-191). / Abstracts in English and Chinese. / ACKNOWLEDGEMENTS --- p.I / ABSTRACT --- p.III / TABLE OF CONTENTS --- p.V / LIST OF FIGURES --- p.X / LIST OF TABLES --- p.XIX / LIST OF ABBREVIATIONS --- p.XXII / Chapter Chapter 1: --- LITERATURE REVIEW --- p.1 / Chapter 1. --- Aristolochia --- p.1 / Chapter 1.1 --- "Aristolochia, as a plant" --- p.1 / Chapter 1.2 --- The chemicals in Aristolochia --- p.1 / Chapter 1.3 --- "Aristolochia, as herbal remedies" --- p.3 / Chapter 1.4 --- The Aristolochia poisoning cases --- p.4 / Chapter 1.5 --- The mechanism of AAs --- p.6 / Chapter 1.6 --- Renaming CHN to AAN --- p.6 / Chapter 1.7 --- Banning Aristolochia herbs --- p.7 / Chapter 1.8 --- The possible cause of ANN --- p.8 / Chapter 1.8.1 --- Misuse of Chinese Medicine --- p.8 / Chapter 1.8.2 --- Substitution --- p.9 / Chapter 1.8.3 --- The complexities of the herbal nomenclature --- p.9 / Chapter 1.8.4 --- Adulteration --- p.11 / Chapter 1.9 --- Methods for authenication --- p.12 / Chapter 1.9.1 --- Traditional methods for authentication --- p.12 / Chapter 1.9.2 --- The advantage of using molecular methods --- p.13 / Chapter 1.9.2.1 --- DNA fingerprinting --- p.13 / Chapter 1.9.2.2 --- DNA sequencing --- p.15 / Chapter 1.10 --- Method selection rationale --- p.15 / Chapter 1.11 --- The need for molecular authentication of six medicinal herbs --- p.17 / Chapter 1.11.1 --- The herb Mutong --- p.17 / Chapter 1.11.1.1 --- The poisoning cases reported --- p.19 / Chapter 1.11.1.2 --- Other authentication studies of Mutong --- p.19 / Chapter 1.11.2 --- The herb Muxiang --- p.20 / Chapter 1.11.2.1 --- Chemical profile --- p.21 / Chapter 1.11.2.2 --- Other authentication studies of Muxiang --- p.21 / Chapter 1.11.3 --- The herb Baiying --- p.22 / Chapter 1.11.3.1 --- The poisoning cases reported --- p.23 / Chapter 1.11.3.2 --- Other authentication studies of Baiying --- p.24 / Chapter 1.11.4 --- The herb Fangj --- p.i 24 / Chapter 1.11.4.1 --- Chemical profile --- p.25 / Chapter 1.11.4.2 --- The poisoning cases reported --- p.26 / Chapter 1.11.5 --- The herb Madouling --- p.26 / Chapter 1.11.6 --- The herb Zhushalian --- p.27 / Chapter 1.12 --- Aristolochia specific markers --- p.28 / Chapter 1.13 --- Significance of the research --- p.29 / Chapter Chapter 2: --- OBJECTIVE --- p.30 / Chapter Chapter 3: --- MATERIALS AND METHODS --- p.31 / Chapter 3.1 --- Samples source --- p.31 / Chapter 3.2 --- Total DNA extraction --- p.39 / Chapter 3.2.1 --- Cetyltriethylammonium bromide extraction --- p.39 / Chapter 3.2.2 --- Commercial kit extraction --- p.40 / Chapter 3.3 --- DNA amplification --- p.42 / Chapter 3.4 --- DNA fingerprinting --- p.43 / Chapter 3.4.1 --- DNA concentration determination --- p.43 / Chapter 3.4.2 --- ISSR fingerprinting --- p.44 / Chapter 3.5 --- Agarose gel electrophoresis --- p.45 / Chapter 3.6 --- Purification of PCR product --- p.46 / Chapter 3.7 --- Cloning of PCR product --- p.47 / Chapter 3.7.1 --- Ligation --- p.47 / Chapter 3.7.2 --- Transformation --- p.48 / Chapter 3.7.3 --- Cell cultivation --- p.48 / Chapter 3.7.4 --- Plasmid extraction --- p.49 / Chapter 3.7.5 --- Insert confirmation --- p.49 / Chapter 3.8 --- DNA sequencing --- p.50 / Chapter 3.8.1 --- Cycle sequencing --- p.50 / Chapter 3.8.2 --- Purification of cycle sequencing product --- p.51 / Chapter 3.8.3 --- DNA analysis --- p.51 / Chapter 3.9 --- Sequence analysis --- p.52 / Chapter Chapter 4: --- AUTHENICATION OF MUTONG --- p.53 / Chapter 4.1 --- Results --- p.53 / Chapter 4.1.1 --- Sequence alignment --- p.54 / Chapter 4.1.1.1 --- trnL-trnF sequences --- p.54 / Chapter 4.1.1.2 --- psbA-trnH sequences --- p.55 / Chapter 4.1.2 --- Percentage similarity analysis --- p.64 / Chapter 4.1.3 --- Dendrogram analysis --- p.67 / Chapter 4.2 --- Discussion --- p.73 / Chapter 4.2.1 --- Evaluation of chloroplast trnL-trnF region in differentiation of Mutong --- p.73 / Chapter 4.2.2 --- Evaluation of chloroplast psbA-trnH region in differentiation of Mutong --- p.74 / Chapter 4.2.3 --- Evaluation of using DNA sequencing in differentiation of Mutong --- p.75 / Chapter 4.3 --- Conclusion --- p.77 / Chapter Chapter 5: --- AUTHENICATION OF MUXIANG --- p.78 / Chapter 5.1 --- Results --- p.78 / Chapter 5.1.1 --- Sequence alignment --- p.79 / Chapter 5.1.1.1 --- trnL-trnF sequences --- p.79 / Chapter 5.1.1.2 --- psbA-trnH sequences --- p.80 / Chapter 5.1.2 --- Percentage similarity analysis --- p.88 / Chapter 5.1.3 --- Dendrogram study --- p.91 / Chapter 5.2 --- Discussion --- p.97 / Chapter 5.2.1 --- Evaluation of chloroplast trnL-trnF region in differentiation of Muxiang --- p.97 / Chapter 5.2.2 --- Evaluation of chloroplast psbA-trnH region in differentiation of Muxiang --- p.99 / Chapter 5.3 --- Conclusion --- p.100 / Chapter Chapter 6: --- AUTHENICATION OF BAIYING --- p.102 / Chapter 6.1 --- Results --- p.102 / Chapter 6.1.1 --- Sequence alignment --- p.103 / Chapter 6.1.2 --- Percentage similarity analysis --- p.107 / Chapter 6.1.3 --- Dendrogram analysis --- p.107 / Chapter 6.2 --- Discussion --- p.109 / Chapter 6.2.1 --- Evaluation of chloroplast psbA-trnH region in differentiation of Solarium and Aristolochia --- p.109 / Chapter 6.2.2 --- Molecular authentication of Baiying --- p.112 / Chapter 6.3 --- Conclusion --- p.113 / Chapter Chapter 7: --- AUTHENICATION OF FANGJI --- p.114 / Chapter 7.1 --- Results --- p.114 / Chapter 7.1.1 --- Sequence alignment --- p.115 / Chapter 7.1.1.1 --- trnL-trnF sequence --- p.115 / Chapter 7.1.1.2 --- psbA-trnH sequence --- p.116 / Chapter 7.1.2 --- Percentage similarity analysis --- p.123 / Chapter 7.1.3 --- Dendrogram study --- p.126 / Chapter 7.2 --- Discussion --- p.132 / Chapter 7.2.1 --- Evaluation of chloroplast trnL-trnF region in differentiation of Fangji --- p.132 / Chapter 7.2.2 --- Evaluation of chloroplast psbA-trnH region in differentiation of Fangji --- p.133 / Chapter 7.3 --- Conclusion --- p.133 / Chapter Chapter 8: --- AUTHENICATION OF MADOULING --- p.135 / Chapter 8.1 --- Results --- p.135 / Chapter 8.1.1 --- Sequence alignment --- p.136 / Chapter 8.1.1.1 --- trnL-trnF sequence --- p.136 / Chapter 8.1.1.2 --- psbA-trnH sequence --- p.136 / Chapter 8.1.2 --- Percentage similarity analysis --- p.143 / Chapter 8.1.3 --- Dendrogram study --- p.146 / Chapter 8.2 --- Discussion --- p.152 / Chapter 8.2.1 --- Evaluation of chloroplast trnL-trnF region in differentiation of Madouling --- p.152 / Chapter 8.2.2 --- Evaluation of chloroplast psbA-trnH region in differentiation of Madouling --- p.153 / Chapter 8.3 --- Conclusion --- p.153 / Chapter Chapter 9: --- AUTHENICATION OF ZHUSHALIAN --- p.155 / Chapter 9.1 --- Results --- p.155 / Chapter 9.1.1 --- Sequence alignment --- p.156 / Chapter 9.1.1.1 --- trnL-trnF sequence --- p.156 / Chapter 9.1.1.2 --- psbA-trnH sequence --- p.157 / Chapter 9.1.2 --- Percentage similarity analysis --- p.157 / Chapter 9.1.3 --- Dendrogram study --- p.162 / Chapter 9.2 --- Discussion --- p.166 / Chapter 9.2.1 --- Evaluation of chloroplast trnL-trnF region in differentiation of Zhushalian --- p.166 / Chapter 9.2.2 --- Evaluation of chloroplast psbA-trnH region in differentiation of Zhushalian --- p.171 / Chapter 9.3 --- Conclusion --- p.171 / Chapter Chapter 10: --- ARISTOLOCHIA SPECIFIC MARKER --- p.172 / Chapter 10.1 --- ISSR fingerprinting --- p.172 / Chapter 10.2 --- Discussion --- p.178 / Chapter Chapter 11: --- CONCLUSION --- p.180 / BIBLIOGRAPHY --- p.182 / APPENDIX - MATERIALS PREPARATION --- p.192

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

Yu, Jing. / "November 2011." / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 161-172). / Abstracts in English and Chinese. / Abstract --- p.I / 摘要 --- p.III / Acknowledgements --- p.V / Contents --- p.VI / List of Figures --- p.VIII / List of Tables --- p.X / Abbreviations and Symbols --- p.XII / Chapter CHAPTER 1 --- Introduction --- p.1 / Chapter 1.1 --- Phylogenetic study of Hedyotis --- p.2 / Chapter 1.1.1 --- Rubiaceae --- p.2 / Chapter 1.1.2 --- Controversial taxonomic issues --- p.9 / Chapter 1.2 --- Traditional Chinese medicine (TCM) --- p.19 / Chapter 1.2.1 --- Introduction --- p.19 / Chapter 1.2.2 --- Baihuasheshecao --- p.20 / Chapter 1.2.3 --- Authentication of Baihuasheshecao --- p.23 / Chapter 1.3 --- Icefishes in the Hong Kong market --- p.23 / Chapter 1.3.1 --- Introduction --- p.23 / Chapter 1.4 --- Molecular approach --- p.25 / Chapter 1.4.1 --- Introduction to molecular phylogeny --- p.25 / Chapter 1.4.2 --- FINS (Forensically Informative Nucleotide Sequencing) for species identification --- p.27 / Chapter 1.4.3 --- DNA sequence markers --- p.28 / Chapter 1.5 --- Objectives --- p.38 / Chapter CHAPTER 2 --- MATERIALS AND METHODOLOGY --- p.41 / Chapter 2.1 --- Materials --- p.42 / Chapter 2.2 --- DNA extraction --- p.50 / Chapter 2.3 --- Polymerase chain reaction (PCR) method --- p.51 / Chapter 2.4 --- Gel electrophoresis --- p.54 / Chapter 2.5 --- PCR production purification --- p.54 / Chapter 2.6 --- Ligation and transformation and transformation of PCR product --- p.56 / Chapter 2.7 --- DNA sequencing and sequence analyses --- p.58 / Chapter CHAPTER 3 --- USING FORENSICALLY INFORMATIVE NUCLEOTIDE SEQUENCING (FINS) TECHNOLOGY FOR SPECIES IDENTIFICATION --- p.64 / Chapter 3.1 --- Authentication of Baihuasheshecao by FINS Analysis --- p.65 / Chapter 3.1.1 --- Authentication using FINS technology --- p.65 / Chapter 3.1.2 --- Relative effectiveness of DNA regions for FINS analysis --- p.70 / Chapter 3.1.3 --- Phylogenetic interpretation --- p.72 / Chapter 3.2 --- Authentication of Salangids (Icefishes) by FINS Analysis --- p.74 / Chapter 3.2.1 --- Analysis based on mitochondrial ribosome DNA region --- p.74 / Chapter 3.2.2 --- Analysis based on mitochondrial 16S rRNA --- p.77 / Chapter 3.2.3 --- Analysis based on combined regions --- p.79 / Chapter 3.2.4 --- Phylogenetic analysis --- p.81 / Chapter 3.2.5 --- Discussion --- p.85 / Chapter 3.3 --- Conclusions --- p.88 / Chapter CHAPTER 4 --- PHYLOGENTIC STUDY OF HEDYOTIS IN CHINA AND THEIR POSITION IN SPERMACOCEAE --- p.89 / Chapter 4.1 --- Phylogentic study of Hedyotis species in Chinese --- p.90 / Chapter 4.1.1 --- Nuclear ITS region --- p.90 / Chapter 4.1.2 --- Plastid trnL intron and trnL-V intergenic spacer region --- p.94 / Chapter 4.1.3 --- Plastid trnH-psbA intergenic spacer region --- p.98 / Chapter 4.1.4 --- Plastid rbcL region --- p.102 / Chapter 4.1.5 --- Plastid matK region --- p.106 / Chapter 4.1.7 --- Combined analysis --- p.114 / Chapter 4.2 --- The phylogenetic position of Hedyotis (species in China) in the tribe of Spermacoceae s.1 --- p.121 / Chapter 4.2.1 --- Plastid trnL - F intergenic spacer region --- p.121 / Chapter 4.2.2 --- Plastid rbcL region --- p.133 / Chapter 4.2.3 --- Plastid rps16 region --- p.141 / Chapter 4.3 --- Discussion --- p.153 / Chapter 4.3.1 --- Comparison of phylogenetic utility of the six DNA regions --- p.153 / Chapter 4.3.2 --- Diplophragma section --- p.154 / Chapter 4.3.3 --- "Hedyotis, Dimetia, Euoldendandia and Gonotheca sections" --- p.156 / Chapter 4.3.4 --- The position of Hedyotis (species in China) in Spermacoceae --- p.158 / Chapter 4.4 --- Conclusions --- p.160 / REFERENCES --- p.161 / APPENDIX --- p.173

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

Li Ming. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 146-161). / Abstracts in English and Chinese. / ACKNOWLEDGEMENTS --- p.I / ABSTRACT --- p.III / TABLE OF CONTENTS --- p.VII / LIST OF FIGURES AND TABLES --- p.XIII / LIST OF ABBREVIATIONS --- p.XX / Chapter CHAPTER ONE --- LITERATURE REVIEW --- p.1 / Chapter 1.1 --- Authentication of Chinese medicines --- p.1 / Chapter 1.1.1 --- The need for authentication of Chinese medicines --- p.1 / Chapter 1.1.2 --- Traditional methods for authentication --- p.2 / Chapter 1.1.3 --- Molecular methods for authentication --- p.4 / Chapter 1.1.3.1 --- DNA fingerprinting --- p.5 / Chapter 1.1.3.2 --- DNA sequencing --- p.6 / Chapter 1.1.3.2.1 --- Choosing a suitable region for DNA sequencing --- p.7 / Chapter 1.1.3.2.2 --- Chloroplast irnL-trnF region --- p.9 / Chapter 1.1.3.2.3 --- Complete sequence of ITS rDNA region --- p.10 / Chapter 1.1.3.2.4 --- 5S rDNA intergenic spacer --- p.11 / Chapter 1.1.3.2.5 --- Calculation of similarities among sequences --- p.12 / Chapter 1.1.3.2.6 --- Construction methods of phylograms --- p.12 / Chapter 1.2 --- The need for molecular authentication of three medicinal herbs --- p.14 / Chapter 1.2.1 --- The herb Baiying --- p.14 / Chapter 1.2.1.1 --- The poisoning case reported in Hong Kong --- p.14 / Chapter 1.2.1.2 --- The identity of genuine Baiying --- p.15 / Chapter 1.2.1.3 --- Morphological characters of the herb Baiying --- p.15 / Chapter 1.2.1.4 --- Medicinal values of Baiying --- p.17 / Chapter 1.2.1.5 --- Xungufeng as the adulterant of Baiying --- p.17 / Chapter 1.2.1.5.1 --- The toxic chemicals aristolochic acids --- p.18 / Chapter 1.2.1.6 --- The need for molecular authentication of Baiying --- p.19 / Chapter 1.2.2 --- The herb Baihuasheshecao --- p.19 / Chapter 1.2.2.1 --- The identity of Baihuasheshecao --- p.19 / Chapter 1.2.2.2 --- Morphological characters of the herb Baihuasheshecao --- p.20 / Chapter 1.2.2.3 --- Medicinal uses --- p.23 / Chapter 1.2.2.4 --- Chemical profile --- p.24 / Chapter 1.2.2.5 --- Adulterants of Baihuasheshecao --- p.24 / Chapter 1.2.2.6 --- Chemical studies of H. diffusa and H. corymbosa --- p.25 / Chapter 1.2.2.7 --- Existing methods for authentication --- p.26 / Chapter 1.2.2.8 --- The need for molecular authentication of Baihuasheshecao --- p.28 / Chapter 1.2.3 --- The herb Chuanlianzi --- p.28 / Chapter 1.2.3.1 --- The identity of Chuanlianzi --- p.28 / Chapter 1.2.3.2 --- Medicinal values --- p.29 / Chapter 1.2.3.3. --- The bioactive chemical --- p.31 / Chapter 1.2.3.4 --- Kulianzi as the substitute of Chuanlianzi --- p.31 / Chapter 1.2.3.5 --- Poisoning cases reported due to ingestion of Kulianzi --- p.32 / Chapter 1.2.3.6 --- Comparative studies of Chuanlianzi and Kulianzi --- p.32 / Chapter 1.2.3.7 --- The need for molecular authentication of Chuanlianzi --- p.33 / Chapter CHAPTER TWO --- OBJECTIVE --- p.35 / Chapter CHAPTER THREE --- MATERIALS AND METHODS --- p.36 / Chapter 3.1 --- Plant and herb samples --- p.36 / Chapter 3.2 --- Total DNA extraction --- p.48 / Chapter 3.2.1 --- Cetyltriethylammonium bromide extraction --- p.48 / Chapter 3.2.2 --- Commercial kit extraction --- p.49 / Chapter 3.3 --- DNA amplification --- p.50 / Chapter 3.4 --- DNA fingerprinting --- p.51 / Chapter 3.4.1 --- DNA concentration determination --- p.51 / Chapter 3.4.2 --- ISSR fingerprinting --- p.52 / Chapter 3.5 --- Agarose gel electrophoresis --- p.53 / Chapter 3.6 --- Purification of PCR product --- p.53 / Chapter 3.7 --- Cloning of PCR product --- p.54 / Chapter 3.7.1 --- Ligation --- p.54 / Chapter 3.7.2 --- Transformation --- p.55 / Chapter 3.7.3 --- Cell cultivation --- p.55 / Chapter 3.7.4 --- Plasmid extraction --- p.55 / Chapter 3.7.5 --- Insert confirmation --- p.56 / Chapter 3.8 --- Determination of DNA concentration --- p.56 / Chapter 3.9 --- DNA sequencing --- p.57 / Chapter 3.9.1 --- Cycle sequencing --- p.57 / Chapter 3.9.2 --- Purification of cycle sequencing products --- p.57 / Chapter 3.9.3 --- DNA analysis --- p.58 / Chapter 3.10 --- Sequence analysis --- p.58 / Chapter CHAPTER FOUR --- MOLECULAR AUTHENTICATION OF BAIYING --- p.59 / Chapter 4.1 --- Results --- p.59 / Chapter 4.1.1 --- Sequence alignment --- p.59 / Chapter 4.1.2 --- Percentage similarity analysis --- p.68 / Chapter 4.1.3 --- Phylogram study --- p.71 / Chapter 4.2 --- Discussion --- p.79 / Chapter 4.2.1 --- Evaluation of chloroplast trnL-trnF region in differentiation of Baiying and Xungufeng --- p.79 / Chapter 4.2.2 --- Molecular authentication of Baiying --- p.80 / Chapter 4.3 --- Conclusion --- p.81 / Chapter CHAPTER FIVE --- MOLECULAR AUTHENTICATION OF BAIHUASHESHECAO --- p.82 / Chapter 5.1 --- Results --- p.82 / Chapter 5.1.1 --- ITS region used for DNA sequencing --- p.82 / Chapter 5.1.2 --- Sequence alignment --- p.82 / Chapter 5.1.3 --- Percentage similarity analysis --- p.88 / Chapter 5.1.4 --- Phylogram study --- p.90 / Chapter 5.2 --- Discussion --- p.98 / Chapter 5.2.1 --- Evaluation of complete sequence of ITS region in differentiation of Hedyotis species --- p.98 / Chapter 5.2.2 --- Molecular authentication of retailed Baihuasheshecao --- p.99 / Chapter 5.2.3 --- Analysis of conflicting data between this study and published results --- p.99 / Chapter 5.2.3.1 --- Comparison of ITS-1 region --- p.101 / Chapter 5.2.3.2 --- Comparison of ITS-2 region --- p.104 / Chapter 5.2.3.3 --- Proposed reasons for the conflicting data --- p.108 / Chapter 5.3 --- Conclusion --- p.109 / Chapter CHAPTER SIX --- MOLECULAR AUTHENTICATION OF CHUANLIANZI --- p.110 / Chapter 6.1 --- Results --- p.110 / Chapter 6.1.1 --- DNA sequencing --- p.110 / Chapter 6.1.1.1 --- Complete sequence of ITS region used for DNA sequencing --- p.110 / Chapter 6.1.1.1.1 --- Sequence alignment --- p.111 / Chapter 6.1.1.1.2 --- Percentage similarity analysis --- p.113 / Chapter 6.1.1.2 --- 5S rDNA intergenic spacer used for DNA sequencing --- p.113 / Chapter 6.1.1.2.1 --- Sequencing alignment --- p.114 / Chapter 6.1.1.2.2 --- Percentage similarity analysis --- p.122 / Chapter 6.1.1.2.3 --- Phylogram study --- p.128 / Chapter 6.1.2 --- ISSR fingerprinting --- p.136 / Chapter 6.2 --- Discussion --- p.138 / Chapter 6.2.1 --- DNA sequencing results --- p.138 / Chapter 6.2.2. --- ISSR fingerprinting results --- p.139 / Chapter 6.2.3 --- Investigation of the identity of retailed Chuanlianzi --- p.140 / Chapter 6.2.4 --- Taxonomic interpretation for Melia species --- p.141 / Chapter 6.2.5 --- Kulianzi involved in this study --- p.141 / Chapter 6.3 --- Conclusion --- p.141 / Chapter CHAPTER SEVEN --- CONCLUSION --- p.143 / BILBIOGRAPHY --- p.146 / APPDENDIX - MATERIAL PREPARATION --- p.162