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

Made available in DSpace on 2014-06-11T19:26:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-07-05Bitstream added on 2014-06-13T19:12:48Z : No. of bitstreams: 1 ribeiro_ao_me_botib.pdf: 1200014 bytes, checksum: e1f590cd087700ef38c4458945aa5242 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Impactos antropogênicos são uma ameaça crescente para a diversidade de peixes, especialmente em áreas próximas a grandes centros urbanos, e muitas ações efetivas de conservação dependem da identificação acurada de espécies. Considerando a utilidade do DNA barcoding como um sistema global de identificação e descoberta de espécies, o presente estudo intenta compilar uma biblioteca referência de sequências barcode para os peixes marinhos das regiões Sudeste e Sul do Brasil, com ênfase no estado de São Paulo. O fragmento barcode padrão de 652 pares de bases do gene citocromo c oxidase subunidade I (COI) foi amplificado por PCR e sequenciado bidirecionalmente para 875 indivíduos pertencentes a 156 espécies. A análise de neighbor-joining revelou que esta abordagem discrimina sem ambiguidade 93,6% das espécies analisadas. A maioria das espécies exibiu baixas distâncias genéticas intraespecíficas (0,40%), cerca de 30 vezes menor que a distância entre espécies congenéricas. Seis espécies apresentaram divergências intraespecíficas entre 2,03 e 12,63%, sugerindo diversidade subestimada. Notavelmente, apenas dois pares de espécies apresentaram divergência menor que 2% entre elas. Esta biblioteca é um primeiro passo para conhecer melhor a diversidade molecular das espécies de peixes marinhos do Sudeste e do Sul do Brasil, fornecendo subsídios para estudos posteriores sobre esta fauna — aumenta a capacidade de identificar as espécies a partir de todos os estágios de vida e mesmo a partir de fragmentos, abre caminhos para uma melhor compreensão acerca das interações entre espécies, auxilia na calibração das estimativas de composição e riqueza das espécies de um ecossitema, e fornece ferramentas para a autenticação de bioprodutos e para o monitoramento da exploração ilegal de espécies / Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centers, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, the present study aims to assemble a DNA barcode reference sequence library for marine fishes from the Southeast and South regions of Brazil, with emphasis on the São Paulo state. The standard 652 base-pair ‘barcode’ fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bi-directionally sequenced from 875 individuals belonging to 156 species. A neighbor-joining analysis revealed that this approach can unambiguously discriminate 93.6% of the species surveyed. Most species exhibited low intra-specific genetic distances (0.40%), about 30-fold less than the distance among species within a genus. Six species showed intra-specific divergences ranging from 2.03 to 12.63%, suggesting overlooked diversity. Notably, just two species-pairs exhibited barcode divergences of less than 2%. This library is a first step to better know the molecular diversity of marine fish species from the Southeast and South regions of Brazil, providing subsidies for further studies in this fauna ― extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating estimatives about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation

Orientador: Claudio de Oliveira / Banca: Mateus Pepinelli / Banca: José Lima de Figueiredo / Resumo: Impactos antropogênicos são uma ameaça crescente para a diversidade de peixes, especialmente em áreas próximas a grandes centros urbanos, e muitas ações efetivas de conservação dependem da identificação acurada de espécies. Considerando a utilidade do DNA barcoding como um sistema global de identificação e descoberta de espécies, o presente estudo intenta compilar uma biblioteca referência de sequências barcode para os peixes marinhos das regiões Sudeste e Sul do Brasil, com ênfase no estado de São Paulo. O fragmento barcode padrão de 652 pares de bases do gene citocromo c oxidase subunidade I (COI) foi amplificado por PCR e sequenciado bidirecionalmente para 875 indivíduos pertencentes a 156 espécies. A análise de neighbor-joining revelou que esta abordagem discrimina sem ambiguidade 93,6% das espécies analisadas. A maioria das espécies exibiu baixas distâncias genéticas intraespecíficas (0,40%), cerca de 30 vezes menor que a distância entre espécies congenéricas. Seis espécies apresentaram divergências intraespecíficas entre 2,03 e 12,63%, sugerindo diversidade subestimada. Notavelmente, apenas dois pares de espécies apresentaram divergência menor que 2% entre elas. Esta biblioteca é um primeiro passo para conhecer melhor a diversidade molecular das espécies de peixes marinhos do Sudeste e do Sul do Brasil, fornecendo subsídios para estudos posteriores sobre esta fauna - aumenta a capacidade de identificar as espécies a partir de todos os estágios de vida e mesmo a partir de fragmentos, abre caminhos para uma melhor compreensão acerca das interações entre espécies, auxilia na calibração das estimativas de composição e riqueza das espécies de um ecossitema, e fornece ferramentas para a autenticação de bioprodutos e para o monitoramento da exploração ilegal de espécies / Abstract: Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centers, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, the present study aims to assemble a DNA barcode reference sequence library for marine fishes from the Southeast and South regions of Brazil, with emphasis on the São Paulo state. The standard 652 base-pair 'barcode' fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bi-directionally sequenced from 875 individuals belonging to 156 species. A neighbor-joining analysis revealed that this approach can unambiguously discriminate 93.6% of the species surveyed. Most species exhibited low intra-specific genetic distances (0.40%), about 30-fold less than the distance among species within a genus. Six species showed intra-specific divergences ranging from 2.03 to 12.63%, suggesting overlooked diversity. Notably, just two species-pairs exhibited barcode divergences of less than 2%. This library is a first step to better know the molecular diversity of marine fish species from the Southeast and South regions of Brazil, providing subsidies for further studies in this fauna ― extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating estimatives about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation / Mestre

Cheung, Chun Wai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 111-128). / Abstracts in English and Chinese. / Acknowledgement --- p.ii / Abstract --- p.iv / 摘要 --- p.vii / Table of content --- p.ix / List of Figures --- p.xvii / List of Tables --- p.xix / Abbreviations --- p.xxi / Chapter Chapter 1. --- Introduction --- p.1 / Chapter 1.1 --- Complementary and Alternative Medicine (CAM) and Traditional Chinese Medicine (TCM) --- p.1 / Chapter 1.2 --- The development of Traditional Chinese Medicine --- p.2 / Chapter 1.3 --- Quality control of Traditional Chinese Medicine --- p.3 / Chapter 1.4 --- Problems of adulteration --- p.5 / Chapter 1.4.1 --- Confusion by common names --- p.5 / Chapter 1.4.2 --- Erroneous and intentional adulteration --- p.6 / Chapter 1.5 --- Authentication of Traditional Chinese Medicine using DNA techniques --- p.7 / Chapter 1.6 --- Crocodile meat --- p.10 / Chapter 1.6.1 --- Crocodile meat as Traditional Chinese Medicine --- p.10 / Chapter 1.6.2 --- Crocodile meat as exotic meat --- p.10 / Chapter 1.6.3 --- Effects of crocodile meat on mice --- p.12 / Chapter 1.6.4 --- Adulteration of crocodile meat in Hong Kong --- p.13 / Chapter 1.6.5 --- Authentication of crocodile meat --- p.14 / Chapter 1.6.5.1 --- SCAR analysis --- p.14 / Chapter 1.6.5.2 --- 12S and 16S ribosomal DNA --- p.14 / Chapter 1.7 --- Fish air-bladder --- p.15 / Chapter 1.7.1 --- Fish air-bladder as Traditional Chinese Medicine --- p.15 / Chapter 1.7.2 --- A case study --- p.16 / Chapter 1.7.3 --- Authentication of fish air-bladder --- p.17 / Chapter 1.8 --- Radix Stellariae --- p.18 / Chapter 1.8.1 --- Stellaria dichotoma L. var. lanceolata Bge --- p.18 / Chapter 1.8.2 --- Radix Stellariae as Traditional Chinese Medicine --- p.19 / Chapter 1.8.3 --- Chemicals in Radix Stellariae and their uses --- p.19 / Chapter 1.8.4 --- Adulteration of Radix Stellariae --- p.20 / Chapter 1.8.5 --- Authentication of Radix Stellariae --- p.21 / Chapter 1.8.5.1 --- Internal Transcribed Spacers (ITS) --- p.21 / Chapter 1.8.5.2 --- trnH-psbA intergenic spacer --- p.23 / Chapter 1.9 --- Objectives --- p.25 / Chapter Chapter 2. --- Materials and Methods --- p.26 / Chapter 2.1 --- Samples used in the study --- p.26 / Chapter 2.1.1 --- Crocodile and monitor lizard samples --- p.26 / Chapter 2.1.2 --- Sequence from NCBI database --- p.26 / Chapter 2.1.3 --- Fish air-bladder samples --- p.30 / Chapter 2.1.4 --- Radix Stellariae samples and samples of related species --- p.33 / Chapter 2.1.5 --- Sequences from NCBI database --- p.33 / Chapter 2.2 --- Reagents and equipments --- p.36 / Chapter 2.2.1 --- Sample preparation and DNA extraction --- p.36 / Chapter 2.2.2 --- Polymerase Chain Reaction --- p.38 / Chapter 2.2.3 --- Agarose gel electrophoresis and Gene Clean --- p.39 / Chapter 2.2.4 --- Cloning --- p.40 / Chapter 2.2.5 --- Cycle sequencing --- p.41 / Chapter 2.3 --- Experimental procedures --- p.42 / Chapter 2.3.1 --- Sample preparation --- p.42 / Chapter 2.3.2 --- DNA extraction --- p.42 / Chapter 2.3.3 --- Polymerase Chain Reaction --- p.44 / Chapter 2.3.4 --- Agarose gel electrophoresis --- p.47 / Chapter 2.3.5 --- Gene Clean --- p.47 / Chapter 2.3.6 --- Cloning --- p.48 / Chapter 2.3.7 --- Cycle sequencing and sequence analyses --- p.51 / Chapter Chapter 3. --- Crocodile meat - Results and Discussion --- p.54 / Chapter 3.1 --- Results --- p.54 / Chapter 3.1.1 --- SCAR analysis --- p.54 / Chapter 3.1.2 --- Sequence analyses --- p.55 / Chapter 3.1.3 --- The dendrograms --- p.56 / Chapter 3.2 --- Discussion --- p.60 / Chapter 3.2.1 --- SCAR as a quick and inexpensive method for the authentication of crocodile meat --- p.60 / Chapter 3.2.2 --- DNA sequencing - A useful tool to identify the source species of the crocodile meat --- p.61 / Chapter 3.2.3 --- Adulteration of crocodile meat in Hong Kong --- p.63 / Chapter 3.2.4 --- Source species of the genuine crocodile meats and the adulterants --- p.63 / Chapter 3.2.5 --- Regulation of labeling of food in Hong Kong --- p.69 / Chapter 3.2.6 --- Source species of the lizard head and tail from AFCD --- p.69 / Chapter 3.3 --- Summary --- p.70 / Chapter Chapter 4. --- Fish air-bladders - Results and Discussion --- p.72 / Chapter 4.1 --- Results --- p.72 / Chapter 4.1.1 --- Identities of sample BH and F1 --- p.73 / Chapter 4.1.2 --- Identity of sample BS --- p.74 / Chapter 4.1.3 --- Identities of samples GD and ZG --- p.74 / Chapter 4.1.4 --- Identity of sample GG --- p.74 / Chapter 4.1.5 --- "Identities of samples HB, HT and SH" --- p.75 / Chapter 4.1.6 --- Identity of sample JL --- p.75 / Chapter 4.1.7 --- Identity of sample MS --- p.76 / Chapter 4.1.8 --- Identity of sample RE --- p.76 / Chapter 4.2 --- Discussion --- p.77 / Chapter 4.2.1 --- Sample RE was confirmed to have originated from rabbit ears --- p.77 / Chapter 4.2.2 --- Identities of the dry fish air-bladders sold in Hong Kong --- p.79 / Chapter 4.2.3 --- Identities of the fresh fish air-bladders sold in Hong Kong --- p.82 / Chapter 4.2.4 --- Limitations of the use of DNA sequences for source species identification --- p.83 / Chapter 4.2.5 --- Variation in prices of fish air-bladders --- p.87 / Chapter 4.3 --- Summary --- p.88 / Chapter Chapter 5. --- Radix Stellariae - Results and Discussion --- p.89 / Chapter 5.1 --- Results --- p.89 / Chapter 5.1.1 --- Sequence analyses --- p.90 / Chapter 5.1.2 --- The dendrograms --- p.90 / Chapter 5.2 --- Discussion --- p.97 / Chapter 5.2.1 --- Identities of the samples obtained from the market --- p.97 / Chapter 5.2.2 --- Identity of sample Sdl4 --- p.97 / Chapter 5.2.3 --- Identities of samples Sd02R and Sd04 --- p.100 / Chapter 5.2.4 --- Myosoton aquaticum in the Stellaria-Myosoton clade --- p.104 / Chapter 5.2.5 --- Medicinal uses of the substitutes of Radix Stellariae --- p.105 / Chapter 5.3 --- Summary --- p.106 / Chapter Chapter 6. --- Conclusion --- p.107 / Reference --- p.111 / Appendix 1. 12S rDNA sequences of crocodilian and Varanus species obtained from NCBI database for sequence analyses --- p.129 / Appendix 2. 16S rDNA sequences of crocodilian and Varanus species obtained from NCBI database for sequence analyses --- p.130 / "Appendix 3. ITS sequences of the species in the genera Arenaria, Myosoton, Silene, and Stellaria obtained from NCBI database for sequence analyses" --- p.131 / Appendix 4. 7rnH-psbA intergenic spacer sequences of Silene species obtained from NCBI database for sequence analyses --- p.132 / Appendix 5. Sequence alignment of 12S rRNA gene sequences of crocodile and monitor lizard samples --- p.133 / Appendix 6. Sequence alignment of 16S rRNA gene sequences of crocodile and lizard samples --- p.141 / Appendix 7. Sequence alignment of coxl sequences of fish air-bladder samples --- p.149 / Appendix 8. Sequence alignment of 12S rRNA gene sequences of fish air-bladder samples --- p.151 / Appendix 9. Sequence alignment of 16S rRNA gene sequences of fish air-bladder samples --- p.153 / Appendix 10. Sequence alignment of coxl region of Vibrio parahaemolyticus and the coxl primers --- p.155 / Appendix 11. Sequence alignment of ITS sequences of Radix Stellariae and related samples --- p.156 / Appendix 12. Sequence alignment of trnH-psbA of Radix Stellariae and related samples --- p.163 / Appendix 13. Search results of coxl sequences of the fish air-bladder samples in BOLD-IDS --- p.167 / Appendix 14. Search results of coxl sequences of the fish air-bladder samples in NCBI nucleotide BLAST --- p.168 / Appendix 15. Search results of 12S rDNA sequences of the fish air-bladder samples in NCBI nucleotide BLAST --- p.169 / Appendix 16. Search results of 16S rDNA sequences of the fish air-bladder samples in NCBI nucleotide BLAST --- p.170 / Appendix 17. Sequence similarities (%) of coxl sequences of the fish air-bladder samples --- p.171 / Appendix 18. Sequence similarities (%) of 12S rDNA sequences of the fish air-bladder samples --- p.172 / Appendix 19. Sequence similarities (%) of 16S rDNA sequences of the fish air-bladder samples --- p.173