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

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在諸多電腦視覺和模式識別的問題中，採集到的圖像和視頻資料通常是高維的。直接計算這些高維資料常常面臨計算可行性和穩定性等方面的困難。然而，現實世界中的資料通常由少數物理因素產生，因而本質上存在退化的結構。例如，它們可以用子空間、子空間的集合、流形或者分層流形等模型來描述。計算並運用這些內在退化結構不僅有助於深入理解問題的本質，而且能夠幫助解決實際應用中的難題。 / 隨著近些年凸優化理論和應用的發展，一些NP難題諸如低稚矩陣的計算和稀疏表示的問題已經有了近乎完美和高效的求解方法。本論文旨在研究如何應用這些技術來計算高維資料中的退化結構，並著重研究子空間和子空間的集合這兩種結構，以及它們在現實應用方面的意義。這些應用包括:人臉圖像的配准、背景分離以及自動植物辨別。 / 在人臉圖像配准的問題中，同一人臉在不同光照下的面部圖像經過逐圖元配准後應位於一個低維的子空間中。基於此假設，我們提出了一個新的圖像配准方法，能夠對某未知人臉的多副不同光照、表情和姿態下的圖像進行聯合配准，使得每一幅面部圖像的圖元與事先訓練的一般人臉模型相匹配。其基本思想是追尋一個低維的且位於一般人臉子空間附近的仿射子空間。相比于傳統的基於外觀模型的配准方法(例如主動外觀模型)依賴于準確的外觀模型的缺點，我們提出的方法僅需要一個一般人臉模型就可以很好地對該未知人臉的多副圖像進行聯合配准，即使該人臉與訓練該模型的樣本相差很大。實驗結果表明，該方法的配准精度在某些情況下接近于理想情形，即：當該目標人臉的模型事先已知時，傳統方法所能夠達到的配准精度。 / In a wide range of computer vision and pattern recognition problems, the captured images and videos often live in high-dimensional observation spaces. Directly computing them may suffer from computational infeasibility and numerical instability. On the other hand, the data in the real world are often generated due to limited number of physical causes, and thus embed degenerate structures in the nature. For instance, they can be modeled by a low-dimensional subspace, a union of subspaces, a manifold or even a manifold stratification. Discovering and harnessing such intrinsic structures not only brings semantic insight into the problems at hand, but also provides critical information to overcome challenges encountered in the practice. / Recent years have witnessed great development in both the theory and application of convex optimization. Efficient and elegant solutions have been found for NP-hard problems such as low-rank matrix recovery and sparse representation. In this thesis, we study the problem of discovering degenerate structures of high-¬dimensional inputs using these techniques. Especially we focus ourselves on low-dimensional subspaces and their unions, and address their application in overcoming the challenges encoun-tered under three practical scenarios: face image alignment, background subtraction and automatic plant identification. / In facial image alignment, we propose a method that jointly brings multiple images of an unseen face into alignment with a pre-trained generic appearance model despite different poses, expressions and illumination conditions of the face in the images. The idea is to pursue an intrinsic affine subspace of the target face that is low-dimensional while at the same time lies close to the generic subspace. Compared with conventional appearance-based methods that rely on accurate appearance mod-els, ours works well with only a generic one and performs much better on unseen faces even if they significantly differ from those for training the generic model. The result is approximately good as that in an idealistic case where a specific model for the target face is provided. / For background subtraction, we propose a background model that captures the changes caused by the background switching among a few configurations, like traffic lights statuses. The background is modeled as a union of low-dimensional subspaces, each characterizing one configuration of the background, and the proposed algorithm automatically switches among them and identifies violating elements as foreground pixels. Moreover, we propose a robust learning approach that can work with foreground-present training samples at the background modeling stage it builds a correct background model with outlying foreground pixels automatically pruned out. This is practically important when foreground-free training samples are difficult to obtain in scenarios such as traffic monitoring. / For automatic plant identification, we propose a novel and practical method that recognizes plants based on leaf shapes extracted from photographs. Different from existing studies that are mostly focused on simple leaves, the proposed method is de-signed to recognize both simple and compound leaves. The key to that is, instead of either measuring geometric features or matching shape features as in conventional methods, we describe leaves by counting on them the numbers of certain shape patterns. The patterns are learned in a way that they form a degenerate polytope (a spe-cial union of affine subspaces) in the feature space, and can simulate, to some extent, the "keys" used by botanists - each pattern reflects a common feature of several dif-ferent species and all the patterns together can form a discriminative rule for recog-nition. Experiments conducted on a variety of datasets show that our algorithm sig-nificantly outperforms the state-of-art methods in terms of recognition accuracy, ef-ficiency and storage, and thus has a good promise for practicing. / In conclusion, our performed studies show that: 1) the visual data with semantic meanings are often not random - although they can be high-dimensional, they typically embed degenerate structures in the observation space. 2) With appropriate assumptions made and clever computational tools developed, these structures can be efficiently and stably calculated. 3) The employment of these intrinsic structures helps overcoming practical challenges and is critical for computer vision and pattern recognition algorithms to achieve good performance. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / 在背景分離的問題中，靜態場景在不同光照情形下的背景可以被描述為一個線性子空間。然而在實際應用中，背景的局部和突然的變化有可能違背此假設，尤其是當背景在幾個狀態之間切換的情形下，例如交通燈在不同組合狀態之間切換。為了解決該問題，本論文中提出了一個新的背景模型，它將背景描述為一些子空間的集合，每個子空間對應一個背景狀態。我們將背景分離的問題轉化為稀疏逼近的問題，因此演算法能夠自動在多個狀態中切換並成功檢測出前景物體。此外，本論文提出了一個魯棒的字典學習方法。在訓練背景模型的過程中，它能夠處理含有前景物體的圖像，並在訓練過程中自動將前景部分去掉。這個優點在難以收集完整背景訓練樣本的應用情形(譬如交通監視等)下有明顯的優勢。 / 在植物種類自動辨別的問題中，本論文中提出了一個新的有效方法，它通過提取和對比植物葉片的輪廓對植物進行識別和分類。不同于傳統的基於測量幾何特徵或者在形狀特徵之間配對的方法，我們提出使用葉子上某些外形模式的數量來表達樹葉。這些模式在特徵空間中形成一個退化的多面體結構(一種特殊的仿射空間的集合)，而且在某種程度上能夠類比植物學中使用的分類檢索表每個模式都反映了一些不同植物的某個共性，例如某種邊緣、某種形狀、某種子葉的佈局等等;而所有模式組合在一起能夠形成具有很高區分度的分類準則。通過對演算法在四個數據庫上的測試，我們發現本論文提出的方法無論在識別精度還是在效率和存儲方面都相比于目前主流方法有顯著提高，因此具有很好的應用性。 / 總之，我們進行的一些列研究說明:(1) 有意義的視覺資料通常是內在相關的，儘管它們的維度可能很高，但是它們通常都具有某種退化的結構。(2) 合理的假設和運用計算工具可以高效、穩健地發現這些結構。(3) 利用這些結構有助於解決實際應用中的難題，且能夠使得電腦視覺和模式識別演算法達到好的性能。 / Zhao, Cong. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 107-121). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Dedication --- p.i / Acknowledgements --- p.ii / Abstract --- p.v / Abstract (in Chinese) --- p.viii / Publication List --- p.xi / Nomenclature --- p.xii / Contents --- p.xiv / List of Figures --- p.xviii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Motivation --- p.1 / Chapter 1.2 --- Background --- p.2 / Chapter 1.2.1 --- Subspaces --- p.3 / Chapter 1.2.2 --- Unions of Subspaces --- p.6 / Chapter 1.2.3 --- Manifolds and Stratifications --- p.8 / Chapter 1.3 --- Thesis Outline --- p.10 / Chapter Chapter 2 --- Joint Face Image Alignment --- p.13 / Chapter 2.1 --- Introduction --- p.14 / Chapter 2.2 --- Related Works --- p.16 / Chapter 2.3 --- Background --- p.18 / Chapter 2.3.1 --- Active Appearance Model --- p.18 / Chapter 2.3.2 --- Multi-Image Alignment using AAM --- p.20 / Chapter 2.3.3 --- Limitations in Practice --- p.21 / Chapter 2.4 --- The Proposed Method --- p.23 / Chapter 2.4.1 --- Two Important Assumptions --- p.23 / Chapter 2.4.2 --- The Subspace Pursuit Problem --- p.27 / Chapter 2.4.3 --- Reformulation --- p.27 / Chapter 2.4.4 --- Efficient Solution --- p.30 / Chapter 2.4.5 --- Discussions --- p.32 / Chapter 2.5 --- Experiments --- p.34 / Chapter 2.5.1 --- Settings --- p.34 / Chapter 2.5.2 --- Results and Discussions --- p.36 / Chapter 2.6 --- Summary --- p.38 / Chapter Chapter 3 --- Background Subtraction --- p.40 / Chapter 3.1 --- Introduction --- p.41 / Chapter 3.2 --- Related Works --- p.43 / Chapter 3.3 --- The Proposed Method --- p.48 / Chapter 3.3.1 --- Background Modeling --- p.48 / Chapter 3.3.2 --- Background Subtraction --- p.49 / Chapter 3.3.3 --- Foreground Object Detection --- p.52 / Chapter 3.3.4 --- Background Modeling by Dictionary Learning --- p.53 / Chapter 3.4 --- Robust Dictionary Learning --- p.54 / Chapter 3.4.1 --- Robust Sparse Coding --- p.56 / Chapter 3.4.2 --- Robust Dictionary Update --- p.57 / Chapter 3.5 --- Experimentation --- p.59 / Chapter 3.5.1 --- Local and Sudden Changes --- p.59 / Chapter 3.5.2 --- Non-structured High-frequency Changes --- p.62 / Chapter 3.5.3 --- Discussions --- p.65 / Chapter 3.6 --- Summary --- p.66 / Chapter Chapter 4 --- Plant Identification using Leaves --- p.67 / Chapter 4.1 --- Introduction --- p.68 / Chapter 4.2 --- Related Works --- p.70 / Chapter 4.3 --- Review of IDSC Feature --- p.71 / Chapter 4.4 --- The Proposed Method --- p.73 / Chapter 4.4.1 --- Independent-IDSC Feature --- p.75 / Chapter 4.4.2 --- Common Shape Patterns --- p.77 / Chapter 4.4.3 --- Leaf Representation by Counts --- p.80 / Chapter 4.4.4 --- Leaf Recognition by NN Classifier --- p.82 / Chapter 4.5 --- Experiments --- p.82 / Chapter 4.5.1 --- Settings --- p.82 / Chapter 4.5.2 --- Performance --- p.83 / Chapter 4.5.3 --- Shared Dictionaries v.s. Shared Features --- p.88 / Chapter 4.5.4 --- Pooling --- p.89 / Chapter 4.6 --- Discussions --- p.90 / Chapter 4.6.1 --- Time Complexity --- p.90 / Chapter 4.6.2 --- Space Complexity --- p.91 / Chapter 4.6.3 --- System Description --- p.92 / Chapter 4.7 --- Summary --- p.92 / Chapter 4.8 --- Acknowledgement --- p.94 / Chapter Chapter 5 --- Conclusion and Future Work --- p.95 / Chapter 5.1 --- Thesis Contributions --- p.95 / Chapter 5.2 --- Future Work --- p.97 / Chapter 5.2.1 --- Theory Side --- p.98 / Chapter 5.2.2 --- Practice Side --- p.98 / Chapter Appendix-I --- Joint Face Alignment Results --- p.100 / Bibliography --- p.107

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