A vinca (Catharanthus roseus) é uma planta perene, arbustiva, pertencente à família Apocinaceae, cujas folhas e raízes possuem propriedades medicinais. A presença de sintoma de mosaico e deformação foliar em plantas dessa espécie, associados com a presença de partículas alongadas e flexuosas, característica de vírus pertencentes ao gênero Potyvirus, conduziu a estudos complementares para a identificação e caracterização desse vírus. No estudo da gama parcial de hospedeiras foram testadas 28 espécies, envolvendo oito famílias botânicas. Catharanthus roseus e Nicotiana benthamiana apresentaram sintomas de mosaico foliar e Chenopodium amaranticolor e C. quinoa apresentaram lesões locais cloróticas nas folhas inoculadas. A transmissão do vírus com afídeos foi avaliada com as espécies Aphis gossypii, Myzus nicotianae e Toxoptera citricidus. Apenas Aphis gossypii e Myzus nicotianae transmitiram o vírus. O antissoro policlonal produzido contra este potyvirus reagiu com o vírus homólogo e com o Passionfruit woodiness virus (PWV) e Cowpea aphid-borne mosaic virus (CABMV), mas não com o Lettuce mosaic virus (LMV), Papaya ringspot virus - type W (PRSV-W), Potato virus Y (PVY) e Zucchini yellow mosaic virus (ZYMV). O peso molecular da proteína capsidial (CP) foi de aproximadamente 34 kDa. A reação de PCR realizada com os oligonucleotídeos universais de potyvirus e oligonucleotídeos específicos posteriomente confeccionados amplificaram três fragmentos de aproximadamente 0,8, 1,0 e 1,4 Kb, os quais após o seqüênciamento geraram um fragmento de 1654 nucleotídeos (nt) da região 3' terminal do genoma, que inclui parte do gene da replicase viral (Nib), a região codificadora completa do gene da proteína capsidial (CP), seguida de 286 nt da região 3' não traduzida (3'NTR). A identidade da seqüência de nucleotídeos do gene da CP variou de 67,0 a 76,0%, quando comparada com as de outros membros da família Potyviridae. A maior identidade foi com o Omphalodes virus Y (76,0%). A identidade dos aminoácidos deduzidos da proteína capsidial variou de 62,0 a 71,0%, sendo a maior com East Asian Passiflora virus (71%). Para a região não traduzida (3'NTR) a identidade variou de 16,8 a 28,6%. Em conjunto esses dados indicam que este vírus é uma nova espécie dentro do gênero Potyvirus, para o qual se propõe o nome de Vírus do mosaico do Catharanthus (Catharanthus mosaic virus - CatMV). / Catharanthus roseus is known as the common periwinkle or Madagascar periwinkle. It is a perennial, evergreen herb in the family Apocynaceae, which was originally native to the island of Madagascar, although both name and classification are contradictory in some literature. The plants grow up to 80 cm high; have glossy, dark green leaves and bloom during summer. The flowers range from white to hot pink to purple. The species has historically been used in popular medicine to treat a wide assortment of human diseases, as it contains more than 150 useful alkaloids. Plants of C. roseus exhibiting mosaic symptoms followed by malformation of the leaf blades and flower variegation were collected from a garden at the University of São Paulo, School of Agriculture (Piracicaba, State of São Paulo, Brazil). Preliminary electron microscopy exams of negatively stained leaf sap revealed that the symptoms were associated with potyvirus-like particles. The objective of the present work was to obtain further biological, immunological and molecular data to better characterize this species of the genus Potyvirus, family Potyviridae. Of 28 plant species from eight botanical families inoculated mechanically with this potyvirus, only C. roseus and Nicotiana benthamiana developed systemic mosaic, whereas Chenopodium amaranticolor and C. quinoa exhibited only chlorotic local lesions. The virus was transmitted by Aphis gossypii and Myzus nicotianae, but not by Toxoptera citricidus. Polyclonal antiserum raised against this potyvirus reacted with the homologous virus, Passion fruit woodiness virus (PWV) and Cowpea aphid borne mosaic virus (CABMV) in PTA-ELISA. The molecular mass of the coat protein (CP) was approximately 34 kDa. RT-PCR from viral RNA amplified a fragment of approximately 1654 nucleotides (nt) at the 3'-terminal of the viral genome, containing portion of the replicase gene (Nib), the entire CP gene and the 3' untranslated region (3'UTR) (286 nt). When the nucleotide sequence of the CP gene was compared with other members of the Potyviridae family, identities varied from 67.0 to 76.0%. The highest identity was with Omphalodes virus Y. Identity of the deduced amino acid of the CP varied from 62.0 to 71.0%, with the highest for East Asian Passiflora virus. For the 3' UTR, identities varied from 16.8 to 28.6%. The name Catharanthus mosaic virus (CatMV) is proposed for this new potyvirus.

This thesis summarizes ways of representation of biological sequences and file formats used for sequence exchange and storage. Next part deals with techniques used for sequence pairwise alignment, followed by extension of these techniques to the problem of multiple sequence alignment. Additional methods are introduced, that are suboptimal, but on the other hand are able to compute results in reasonable time. Practical part of this thesis consists of implementing multiple sequence alignment application in Java programming language.

No description available.

No / Biarylpyrimidines are characterized as selective ligands for higher-order nucleic acid structures. A concise and efficient synthesis has been devised incorporating Suzuki biaryl cross-coupling of dihalopyrimidines. Two ligand series are described based on the parent thioether 4,6-bis[4-[[2-(dimethylamino)ethyl]mercapto]-phenyl]pyrimidine (la) and amide 4,6-bis(4[(2-(dimethylamino)ethyl)carboxamido]phenyl)pyrimidine (2a) compounds. In UV thermal denaturation studies with the poly(dA)·[poly(dT)]2 triplex structure, thioethers showed stabilization of the triplex form (¿Tm ¿ 20 °C). In contrast, amides showed duplex stabilization (¿Tm ¿ 15 °C) and either negligible stabilization or specific destabilization (¿Tm = -5 °C) of the triplex structure. Full spectra of nucleic acid binding preferences were determined by competition dialysis. The strongest interacting thioether bound preferentially to the poly(dA)·[poly(dT)]2 triplex, Kapp = 1.6 x 105 M-1 (40 x Kapp for CT DNA duplex). In contrast, the strongest binding amide selected the (T2G20T2)4 quadruplex structure, Kapp = 0.31 x 105 M-1 (6.5 x Kapp for CT DNA duplex).

Shum Ka Chiu. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 174-182). / Abstracts in English and Chinese. / Acknowledgement --- p.ii / Abstract --- p.iii / 摘要 --- p.vi / Table of content --- p.viii / List of figures --- p.xvi / List of tables --- p.xxii / Abbreviations --- p.xxv / Chapter Chapter 1. --- Introduction --- p.1 / Chapter 1.1 --- Importance of authentication of Traditional Chinese Medicines --- p.1 / Chapter 1.1.1 --- Confusing nomenclatures --- p.1 / Chapter 1.1.2 --- Similar morphologies of different medicinal materials --- p.2 / Chapter 1.1.3 --- Toxicities of medicinal materials --- p.2 / Chapter 1.1.4 --- Conservation of natural products --- p.2 / Chapter 1.2 --- TCM listed in the Pharmacopoeia of People's Republic of China --- p.3 / Chapter 1.3 --- Overview of mis-use and intoxication of TCM --- p.4 / Chapter 1.4 --- Ordinances regulating Chinese medicines as natural products --- p.7 / Chapter 1.4.1 --- Laws governing Chinese medicine --- p.7 / Chapter 1.4.2 --- Laws governing endangered species --- p.8 / Chapter 1.5 --- Current technologies in the authentication of Traditional Chinese Medicines and their limitations --- p.9 / Chapter 1.6 --- Historical applications of Radix Aconiti --- p.12 / Chapter 1.7 --- Modern applications of Radix Aconiti --- p.16 / Chapter 1.8 --- Research on Radix Aconiti and its chemical components --- p.17 / Chapter 1.8.1 --- Chemistry --- p.17 / Chapter 1.8.2 --- Pharmacology --- p.19 / Chapter 1.8.3 --- Molecular interaction --- p.22 / Chapter 1.9 --- Brief review on the systematics and phylogeny of Aconitum --- p.23 / Chapter 1.10 --- Historical applications of Radix Aucklandiae and related materials --- p.25 / Chapter 1.11 --- Modern applications of Radix Aucklandiae and related material --- p.27 / Chapter 1.12 --- Research on Aucklandiae and related material and their chemical components --- p.28 / Chapter 1.12.1 --- Chemistry --- p.28 / Chapter 1.12.2 --- Pharmacology --- p.29 / Chapter 1.13 --- Brief review on the systematics and phylogeny of Aucklandia and related medicinal species --- p.31 / Chapter 1.14 --- Authentication by DNA sequencing --- p.33 / Chapter 1.14.1 --- Introduction --- p.33 / Chapter 1.14.2 --- Criteria of sequence markers --- p.36 / Chapter 1.14.3 --- Model used to process polymorphism in DNA sequences --- p.37 / Chapter 1.15 --- Screening for novel markers --- p.38 / Chapter 1.15.1 --- Reason for screening novel markers --- p.38 / Chapter 1.15.2 --- Basic principle --- p.39 / Chapter 1.16 --- Introduction to gas chromatography- mass spectrometry --- p.40 / Chapter 1.16.1 --- Basic principles and components of GC-MS --- p.41 / Chapter 1.16.2 --- Advantages and limitations of GC-MS --- p.42 / Chapter 1.16.3 --- Usage of GC-MS on natural product analysis --- p.43 / Chapter 1.16.4 --- Chemometric analysis --- p.44 / Chapter 1.17 --- Objectives --- p.46 / Chapter Chapter 2. --- Materials and Methods --- p.47 / Chapter 2.1 --- Plant samples --- p.47 / Chapter 2.1.1 --- Samples of Aconitum --- p.47 / Chapter 2.1.2 --- Samples of Aucklandia and related species --- p.51 / Chapter 2.2 --- DNA extraction method --- p.58 / Chapter 2.2.1 --- Reagents --- p.58 / Chapter 2.2.2 --- Methods --- p.59 / Chapter 2.3 --- Chemical extraction methods --- p.61 / Chapter 2.4 --- Chemical standard extraction and purification method --- p.62 / Chapter 2.5 --- DNA sequencing --- p.63 / Chapter 2.5.1 --- Reagents --- p.63 / Chapter 2.5.2 --- Methods --- p.65 / Chapter 2.6 --- Genomic subtraction --- p.70 / Chapter 2.7 --- Search for species-specific markers from the subtraction library --- p.74 / Chapter 2.8 --- Gas chromatography- mass spectrometry --- p.74 / Chapter 2.9 --- GC-MS chemometric analysis --- p.75 / Chapter Chapter 3. --- Authentication of Aconitum by DNA Sequencing --- p.76 / Chapter 3.1 --- Introduction --- p.76 / Chapter 3.2 --- Methods --- p.77 / Chapter 3.3 --- Results - 5S spacer --- p.77 / Chapter 3.3.1 --- Sequence information --- p.77 / Chapter 3.3.2 --- Sequence similarity --- p.78 / Chapter 3.3.3 --- Phylogram study --- p.81 / Chapter 3.4 --- Results -psbA-trnH --- p.85 / Chapter 3.4.1 --- Sequence information --- p.85 / Chapter 3.4.2 --- Sequence similarity --- p.85 / Chapter 3.4.3 --- Phylogram study --- p.87 / Chapter 3.5 --- Discussion --- p.91 / Chapter 3.5.1 --- Overview of nuclear ribosomal 5S spacer --- p.91 / Chapter 3.5.2 --- Extensive polymorphism of 5S spacer --- p.91 / Chapter 3.5.3 --- Distribution of samples in the phylograms constructed by 5S spacer --- p.93 / Chapter 3.5.4 --- Utility of 5S spacer for authentication --- p.94 / Chapter 3.5.5 --- Overview of psbA-trnH spacer --- p.94 / Chapter 3.5.6 --- Distribution of samples in the phylograms constructed by psbA-trnH spacer --- p.95 / Chapter 3.5.7 --- A distinctive region of inversion --- p.96 / Chapter 3.5.8 --- Utility of psbA-trnH for authentication --- p.97 / Chapter Chapter 4. --- Screening for Novel Markers for Authentication of Aconitum --- p.98 / Chapter 4.1 --- Introduction --- p.98 / Chapter 4.2 --- Methods --- p.99 / Chapter 4.3 --- Results - subtracted clones --- p.99 / Chapter 4.4 --- Results - SSH6 --- p.104 / Chapter 4.4.1 --- Sequence information --- p.104 / Chapter 4.4.2 --- Sequence similarity --- p.105 / Chapter 4.5 --- Results-SSH15 --- p.107 / Chapter 4.5.1 --- Sequence information --- p.107 / Chapter 4.5.2 --- Sequence similarity --- p.107 / Chapter 4.5.3 --- Phylogram study --- p.109 / Chapter 4.6 --- Results-SSH45 --- p.113 / Chapter 4.6.1 --- Sequence information --- p.113 / Chapter 4.6.2 --- Sequence similarity --- p.113 / Chapter 4.6.3 --- Phylogram study --- p.115 / Chapter 4.7 --- Discussion --- p.119 / Chapter 4.7.1 --- Utility of subtraction in screening markers --- p.119 / Chapter 4.7.2 --- SSH6 --- p.121 / Chapter 4.7.3 --- SSH15 --- p.122 / Chapter 4.7.4 --- SSH45 --- p.123 / Chapter 4.7.5 --- Hybridization in Aconitum --- p.124 / Chapter 4.7.6 --- Inferring species identities of samples from the market --- p.126 / Chapter 4.8 --- Conclusion --- p.128 / Chapter Chapter 5. --- Assessment of Aucklandia lappa and Related Species by GC-MS --- p.129 / Chapter 5.1 --- Introduction --- p.129 / Chapter 5.2 --- Methods --- p.130 / Chapter 5.3 --- Results --- p.130 / Chapter 5.3.1 --- Extraction of essential oil --- p.130 / Chapter 5.3.2 --- GC-MS analysis --- p.131 / Chapter 5.3.3 --- Peak alignment and hierarchical cluster analysis --- p.133 / Chapter 5.3.4 --- Purification of chemical markers from Aucklandia lappa --- p.148 / Chapter 5.3.5 --- Standardization of the purified chemical markers --- p.148 / Chapter 5.3.6 --- Quantitative analysis of chemical markers --- p.152 / Chapter 5.4 --- Discussion --- p.154 / Chapter 5.4.1 --- Analysis of chemical composition --- p.154 / Chapter 5.4.2 --- A comparison on chemometric methods --- p.154 / Chapter 5.4.3 --- Similarity of chemical profiles --- p.156 / Chapter 5.4.4 --- Dendrogram analysis --- p.157 / Chapter 5.4.5 --- Utility of GC-MS in authentication of A. lappa and related species --- p.159 / Chapter 5.4.6 --- Limitations --- p.159 / Chapter 5.4.7 --- Comparison with molecular data --- p.161 / Chapter 5.4.8 --- Contents of dehydrocostuslactone and costunolide --- p.163 / Chapter 5.4.9 --- Locality study --- p.164 / Chapter 5.5 --- Conclusion --- p.165 / Chapter Chapter 6. --- General Discussion --- p.167 / Chapter 6.1 --- DNA sequencing --- p.168 / Chapter 6.2 --- Genomic subtraction --- p.169 / Chapter 6.3 --- Future work on molecular authentication --- p.170 / Chapter 6.4 --- Future work on authentication of Aconitum --- p.170 / Chapter 6.5 --- Gas chromatography- mass spectrometry --- p.171 / Chapter 6.6 --- Future work on authentication by GC-MS --- p.172 / Chapter 6.7 --- Future work on authentication of Aucklandia lappa and related species … --- p.173 / References --- p.174 / Appendix A. Sequence Alignment of 5S Spacer from Aconitum Species --- p.183 / Appendix B. Sequence Alignment of psbA- trnH Spacer from Aconitum Species --- p.188 / Appendix C. Sequences of Subtracted Clones from Aconitum --- p.191 / Appendix D. Sequence Alignment of SSH6 from Aconitum Species --- p.194 / Appendix E. Sequence Alignment of SSH15 from Aconitum Species --- p.195 / Appendix F. Sequence Alignment of SSH45 from Aconitum Species --- p.200 / Appendix G. Gas Chromatograms of Essential Oil Extracts of Aucklandia lappa and Related Species --- p.202

Tse, Sui Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 95-104). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgement --- p.v / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Motivation --- p.1 / Chapter 1.1.1 --- Basic Concepts and Definitions --- p.2 / Chapter 1.2 --- Evolutionary Algorithms --- p.5 / Chapter 1.2.1 --- Chromosome Encoding --- p.6 / Chapter 1.2.2 --- Selection --- p.7 / Chapter 1.2.3 --- Crossover --- p.9 / Chapter 1.2.4 --- Mutation --- p.10 / Chapter 1.2.5 --- Elitism --- p.11 / Chapter 1.2.6 --- Niching --- p.11 / Chapter 1.2.7 --- Population Manipulation --- p.13 / Chapter 1.2.8 --- Building Blocks --- p.13 / Chapter 1.2.9 --- Termination Conditions --- p.14 / Chapter 1.2.10 --- Co-evolution --- p.14 / Chapter 1.3 --- Local Search --- p.15 / Chapter 1.4 --- Memetic Algorithms --- p.16 / Chapter 1.5 --- Objective --- p.17 / Chapter 1.6 --- Summary --- p.17 / Chapter 2 --- Background --- p.18 / Chapter 2.1 --- Multiple Drugs Tumor Chemotherapy --- p.18 / Chapter 2.2 --- Bioinformatics --- p.22 / Chapter 2.2.1 --- Basics of Bioinformatics --- p.24 / Chapter 2.2.2 --- Applications on Biomedical Systems --- p.26 / Chapter 3 --- A New Drug Administration Dynamic Model --- p.29 / Chapter 3.1 --- Three Drugs Mathematical Model --- p.31 / Chapter 3.1.1 --- Rate of Change of Different Subpopulations --- p.32 / Chapter 3.1.2 --- Rate of Change of Different Drug Concen- trations --- p.35 / Chapter 3.1.3 --- Toxicity Effects --- p.35 / Chapter 3.1.4 --- Summary --- p.36 / Chapter 4 --- Memetic Algorithm - Iterative Dynamic Program- ming (MA-IDP) --- p.38 / Chapter 4.1 --- Problem Formulation: Optimal Control Problem (OCP) for Mutlidrug Optimization --- p.38 / Chapter 4.2 --- Proposed Memetic Optimization Algorithm --- p.40 / Chapter 4.2.1 --- Iterative Dynamic Programming (IDP) . . --- p.40 / Chapter 4.2.2 --- Adaptive Elitist-population-based Genetic Algorithm (AEGA) --- p.44 / Chapter 4.2.3 --- Memetic Algorithm 一 Iterative Dynamic Programming (MA-IDP) --- p.50 / Chapter 4.3 --- Summary --- p.56 / Chapter 5 --- MA-IDP: Experiments and Results --- p.57 / Chapter 5.1 --- Experiment Settings --- p.57 / Chapter 5.2 --- Optimization Results --- p.61 / Chapter 5.3 --- Extension to Other Mutlidrug Scheduling Model . --- p.62 / Chapter 5.4 --- Summary --- p.65 / Chapter 6 --- DNA Sequencing by Hybridization (SBH) --- p.66 / Chapter 6.1 --- Problem Formulation: Reconstructing a DNA Sequence from Hybridization Data --- p.70 / Chapter 6.2 --- Proposed Memetic Optimization Algorithm --- p.71 / Chapter 6.2.1 --- Chromosome Encoding --- p.71 / Chapter 6.2.2 --- Fitness Function --- p.73 / Chapter 6.2.3 --- Crossover --- p.74 / Chapter 6.2.4 --- Hill Climbing Local Search for Sequencing by Hybridization --- p.76 / Chapter 6.2.5 --- Elitism and Diversity --- p.79 / Chapter 6.2.6 --- Outline of Algorithm: MA-HC-SBH --- p.81 / Chapter 6.3 --- Summary --- p.82 / Chapter 7 --- DNA Sequencing by Hybridization (SBH): Experiments and Results --- p.83 / Chapter 7.1 --- Experiment Settings --- p.83 / Chapter 7.2 --- Experiment Results --- p.85 / Chapter 7.3 --- Summary --- p.89 / Chapter 8 --- Conclusion --- p.90 / Chapter 8.1 --- Multiple Drugs Cancer Chemotherapy Schedule Optimization --- p.90 / Chapter 8.2 --- Use of the MA-IDP --- p.91 / Chapter 8.3 --- DNA Sequencing by Hybridization (SBH) --- p.92 / Chapter 8.4 --- Use of the MA-HC-SBH --- p.92 / Chapter 8.5 --- Future Work --- p.93 / Chapter 8.6 --- Item Learned --- p.93 / Chapter 8.7 --- Papers Published --- p.94 / Bibliography --- p.95

Chen, Zhang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (p. 109-114). / Abstracts in English and Chinese. / ABSTRACT --- p.I / 摘要 --- p.III / ACKNOWLEDGEMENTS --- p.IV / PUBLICATIONS --- p.VI / CONTRIBUTORS --- p.VII / TABLE OF CONTENTS --- p.VIII / LIST OF TABLES --- p.XIII / LIST OF FIGURES --- p.XIV / LIST OF ABBREVIATIONS --- p.XVI / Chapter SECTION I : --- BACKGROUND --- p.1 / Chapter CHAPTER 1: --- PRENATAL DIAGNOSIS OF FETAL TRISOMY BY NEXT GENERATION SEQUENCING TECHNOLOGY --- p.2 / Chapter 1.1 --- FETAL TRISOMY --- p.2 / Chapter 1.2 --- CONVENTIONAL PRENATAL DIAGNOSIS OF FETAL TRISOMIES --- p.3 / Chapter 1.3 --- CELL FREE FETAL D N A AND ITS APPLICATION IN PRENATAL DIAGNOSIS --- p.5 / Chapter 1.4 --- NEXT GENERATION SEQUENCING TECHNOLOGY --- p.5 / Chapter 1.5 --- SUBSTANTIAL BIAS IN THE NEXT GENERATION SEQUENCING PLATFORM --- p.9 / Chapter 1.6 --- PRENATAL DIAGNOSIS OF TRISOMY BY NEXT GENERATION SEQUENCING --- p.10 / Chapter 1.7 --- AIMS OF THIS THESIS --- p.11 / Chapter SECTION I I : --- MATERIALS AND METHODS --- p.13 / Chapter CHAPTER 2: --- METHODS FOR NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY MATERNAL PLASMA DNA SEQUENCING --- p.14 / Chapter 2.1 --- STUDY DESIGN AND PARTICIPANTS --- p.14 / Chapter 2.1.1 --- Ethics Statement --- p.14 / Chapter 2.1.2 --- "Study design, setting and participants" --- p.14 / Chapter 2.2 --- MATERNAL PLASMA D N A SEQUENCING --- p.17 / Chapter 2.3 --- SEQUENCING DATA ANALYSIS --- p.18 / Chapter SECTION I I I : --- TRISOMY 13 AND 18 DETECTION BY THE T21 BIOINFORMATICS ANALYSIS PIPELINE --- p.21 / Chapter CHAPTER 3: --- THE T21 BIOINFORMATICS ANALYSIS PIPELINE FOR TRISOMY 13 AND 18 DETECTION --- p.22 / Chapter 3.1 --- INTRODUCTION --- p.22 / Chapter 3.2 --- METHODS --- p.23 / Chapter 3.2.1 --- Bioinformatics analysis pipeline for trisomy 13 and 18 detection --- p.23 / Chapter 3.3 --- RESULTS --- p.23 / Chapter 3.3.1 --- Performance of the T21 bioinformatics analysis pipeline for trisomy 13 and 18 detection --- p.23 / Chapter 3.3.2 --- The precision of quantifying chrl 3 and chrl 8 --- p.27 / Chapter 3.4 --- DISCUSSION --- p.29 / Chapter SECTION IV : --- IMPROVING THE T21 BIOINFORMATICS ANALYSIS PIPELINE FOR TRISOMY 13 AND 18 DETECTION --- p.30 / Chapter CHAPTER 4: --- IMPROVING THE ALIGNMENT --- p.31 / Chapter 4.1 --- INTRODUCTION --- p.31 / Chapter 4.2 --- METHODS --- p.32 / Chapter 4.2.1 --- Allowing mismatches in the index sequences --- p.32 / Chapter 4.2.2 --- Calculating the mappability of the human reference genome --- p.33 / Chapter 4.2.3 --- Aligning reads to the non-repeat masked human reference genome --- p.34 / Chapter 4.2.4 --- Trisomy 13 and 18 detection --- p.34 / Chapter 4.3 --- RESULTS --- p.34 / Chapter 4.3.1 --- Increasing read numbers by allowing mismatches in the index sequences --- p.34 / Chapter 4.3.2 --- Increasing read numbers by using the non-masked reference genome for alignment . --- p.38 / Chapter 4.3.3 --- Allowing mismatches in the read alignment --- p.42 / Chapter 4.3.4 --- The performance of trisomy 13 and 18 detection after improving the alignment --- p.47 / Chapter 4.4 --- DISCUSSION --- p.50 / Chapter CHAPTER 5: --- REDUCING THE GC BIAS BY CORRECTION OF READ COUNTS --- p.53 / Chapter 5.1 --- INTRODUCTION --- p.53 / Chapter 5.2 --- METHODS --- p.54 / Chapter 5.2.1 --- Read alignment --- p.54 / Chapter 5.2.2 --- Calculating the correlation between GC content and read counts --- p.55 / Chapter 5.2.3 --- GC correction in read counts --- p.55 / Chapter 5.2.4 --- Trisomy 13 and 18 detection --- p.56 / Chapter 5.3 --- RESULTS --- p.56 / Chapter 5.3.1 --- GC bias in plasma DNA sequencing --- p.56 / Chapter 5.3.2 --- Correcting the GC bias in read counts by linear regression --- p.59 / Chapter 5.3.3 --- Correcting the GC bias in read counts by LOESS regression --- p.65 / Chapter 5.3.4 --- Bin size --- p.72 / Chapter 5.4 --- DISCUSSION --- p.75 / Chapter CHAPTER 6: --- REDUCING THE GC BIAS BY MODIFYING THE GENOMIC REPRESENTATION CALCULATION --- p.77 / Chapter 6.1 --- INTRODUCTION --- p.77 / Chapter 6.2 --- METHODS --- p.78 / Chapter 6.2.1 --- Modifying the genomic representation calculation --- p.78 / Chapter 6.2.2 --- Trisomy 13 and 18 detection --- p.78 / Chapter 6.2.3 --- Combining GC correction and modified genomic representation --- p.78 / Chapter 6.3 --- RESULTS --- p.79 / Chapter 6.3.1 --- Reducing the GC bias by modifying genomic representation calculation --- p.79 / Chapter 6.3.2 --- Combining GC correction and modified genomic representation --- p.86 / Chapter 6.4 --- DISCUSSION --- p.89 / Chapter CHAPTER 7: --- IMPROVING THE STATISTICS FOR TRISOMY 13 AND 18 DETECTION --- p.91 / Chapter 7.1 --- INTRODUCTION --- p.91 / Chapter 7.2 --- METHODS --- p.92 / Chapter 7.2.1 --- Comparing chrl 3 or chrl8 with other chromosomes within the sample --- p.92 / Chapter 7.2.2 --- Comparing chrl 3 or chrl 8 with the artificial chromosomes --- p.92 / Chapter 7.3 --- RESULTS --- p.93 / Chapter 7.3.1 --- Determining the trisomy 13 and 18 status by comparing chromosomes within the samples --- p.93 / Chapter 7.3.2 --- Determining the trisomy 13 and 18 status by comparing chrl3 or chrl 8 with artificial chromosomes --- p.97 / Chapter 7.4 --- DISCUSSION --- p.100 / Chapter SECTION V : --- CONCLUDING REMARKS --- p.102 / Chapter CHAPTER 8: --- CONCLUSION AND FUTURE PERSPECTIVES --- p.103 / Chapter 8.1 --- THE PERFORMANCE OF THE T21 BIOINFORMATICS ANALYSIS PIPELINE DEVELOPED FOR TRISOMY 21 DETECTION IS SUBOPTIMAL FOR TRISOMY 13 AND 18 DETECTION --- p.103 / Chapter 8.2 --- THE ALIGNMENT COULD BE IMPROVED BY ALLOWING ONE MISMATCH IN THE INDEX AND USING THE NON-REPEAT MASKED HUMAN REFERENCE GENOME AS THE ALIGNMENT REFERENCE --- p.104 / Chapter 8.3 --- THE PRECISION OF QUANTIFYING CHR13 AND CHR18 COULD BE IMPROVED BY THE G C CORRECTION OR THE MODIFIED GENOMIC REPRESENTATION --- p.104 / Chapter 8.4 --- THE STATISTICS FOR TRISOMY 13 AND 18 DETECTION COULD BE IMPROVED BY COMPARING CHR13 OR CHR18 WITH ARTIFICIAL CHROMOSOMES WITHIN THE SAMPLE --- p.105 / Chapter 8.5 --- PROSPECTS FOR FUTURE WORK --- p.106 / REFERENCE --- p.109

Wong Ka Lok. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 121-129). / Abstracts in English and Chinese. / Acknowledgments --- p.i / Abstract --- p.ii / Table A --- p.v / Table B --- p.vi / Table of Contents --- p.vii / Abbreviations --- p.xi / Chapter Chapter 1 --- Molecular authentication of endangered crocodiles and snakes / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Traditional method of snake and crocodile identification / Chapter 1.2.1 --- Morphology --- p.7 / Chapter 1.2.2 --- Chemical Analysis --- p.9 / Chapter 1.3 --- Molecular Technology in Authentication / Chapter 1.3.1 --- Polymerase Chain Reactions (PCRs) --- p.11 / Chapter 1.3.2 --- Random-primed amplification reaction --- p.12 / Chapter 1.3.3 --- Sequence Characterized Amplified Region (SCAR) --- p.13 / Chapter 1.3.4 --- PCR-RFLP --- p.13 / Chapter 1.3.5 --- DNA sequencing --- p.14 / Chapter 1.4 --- Objectives and strategies of the study --- p.15 / Chapter Chapter 2 --- Materials and General Methods / Chapter 2.1 --- Reagents and Buffers / Chapter 2.1.1 --- Buffers for Total DNA Extraction --- p.17 / Chapter 2.1.2 --- Reagents for Agarose Gel Electrophoresis --- p.17 / Chapter 2.1.3 --- Reagents for Plasmid DNA Preparation --- p.18 / Chapter 2.1.4 --- Medium for Bacterial Culture --- p.18 / Chapter 2.1.5 --- Reagents for Preparation of Competent Cells --- p.19 / Chapter 2.2 --- DNA Isolation / Chapter 2.2.1 --- Extraction of DNA from meats --- p.20 / Chapter 2.2.2 --- Extraction of DNA from blood --- p.20 / Chapter 2.3 --- Phenol/Chloroform Extraction --- p.21 / Chapter 2.4 --- Ethanol Precipitation --- p.22 / Chapter 2.5 --- DNA Concentration/Purity Estimation --- p.22 / Chapter 2.6 --- Mitochondrial DNA amplification --- p.23 / Chapter 2.7 --- Random-Primed Polymerase Chain Reactions --- p.24 / Chapter 2.8 --- SCAR for Snake samples --- p.24 / Chapter 2.9 --- SCAR for Crocodile samples --- p.25 / Chapter 2.10 --- Restriction fragment length polymorphism analysis --- p.25 / Chapter 2.11 --- Agarose Gel Electrophoresis of DNA --- p.26 / Chapter 2.12 --- Purification of PCR product --- p.26 / Chapter 2.13 --- Preparation of Escherichia coli Competent Cells --- p.27 / Chapter 2.14 --- Ligation and transformation of E. coli --- p.27 / Chapter 2.15 --- Plasmid preparation --- p.28 / Chapter 2.16 --- Screening of Plasmid DNA by Restriction Digestion --- p.29 / Chapter Chapter 3 --- DNA sequencing of snakes & construction of snake database / Chapter 3.1 --- Introduction --- p.30 / Chapter 3.2 --- Materials and methods / Chapter 3.2.1 --- Snake samples --- p.32 / Chapter 3.2.2 --- "DNA Extraction, mitochondrial gene amplification and DNA sequencing" --- p.33 / Chapter 3.2.3 --- Construction of database --- p.33 / Chapter 3.3 --- Results / Chapter 3.3.1 --- Cytochrome b gene amplification and sequencing --- p.34 / Chapter 3.3.2 --- Gene amplification and sequencing of 16S rRNA --- p.42 / Chapter 3.3.3 --- Cytochrome b sequence database --- p.50 / Chapter 3.3.4 --- 16S rRNA sequence database --- p.53 / Chapter 3.4 --- Discussion / Chapter 3.4.1 --- Cytochrome b and 16S rRNA genes of snake species --- p.55 / Chapter 3.4.2 --- Cytochrome b and 16S rRNA databases --- p.55 / Chapter Chapter 4 --- Application of PCR-RFLP and SCAR in snake species identification / Chapter 4.1 --- Introduction --- p.57 / Chapter 4.2 --- Material and Methods / Chapter 4.2.1 --- DNA extraction and PCR-RFLP --- p.58 / Chapter 4.2.2 --- RAPD and SCAR --- p.58 / Chapter 4.3 --- Results / Chapter 4.3.1 --- PCR-RFLP of cytochrome b genes of snakes --- p.59 / Chapter 4.3.2 --- PCR-RFLP of 16S rDNA --- p.61 / Chapter 4.3.3 --- RAPD & SCAR analysis --- p.67 / Chapter 4.4 --- Discussion --- p.72 / Chapter Chapter 5 --- "Application of DNA sequencing, PCR-RFLP and SCAR to identify crocodile species" / Chapter 5.1 --- Introduction --- p.74 / Chapter 5.2 --- Materials and methods / Chapter 5.2.1 --- "Crocodile, human and four animal samples" --- p.75 / Chapter 5.2.2 --- "DNA Extraction, mitochondrial gene amplification and DNA sequencing" --- p.75 / Chapter 5.2.3 --- PCR-RFLP and SCAR --- p.76 / Chapter 5.3 --- Results / Chapter 5.3.1 --- Isolation of crocodiles DNA --- p.77 / Chapter 5.3.2 --- Isolation of DNA from Human and four animal species --- p.78 / Chapter 5.3.3 --- Cytochrome b gene amplification and sequencing --- p.78 / Chapter 5.3.4 --- 16S rRNA gene amplification and sequencing --- p.84 / Chapter 5.3.5 --- PCR-RFLP of cytochrome b --- p.89 / Chapter 5.3.6 --- PCR-RFLP of 16S rRNA --- p.91 / Chapter 5.3.7 --- SCAR primers for four crocodile species --- p.93 / Chapter 5.4 --- Discussion --- p.97 / Chapter Chapter 6 --- A case report - authentication of animal samples using DNA sequencing / Chapter 6.1 --- Introduction --- p.99 / Chapter 6.2 --- Material and methods / Chapter 6.2.1 --- Materials --- p.101 / Chapter 6.2.2 --- DNA Extraction and sequencing --- p.101 / Chapter 6.3 --- Result and discussion / Chapter 6.3.1 --- Cytochrome b gene sequencing --- p.102 / Chapter 6.3.2 --- Sequence homology among samples and meats obtained from the market --- p.111 / Chapter 6.3.3 --- Identity of samples B & D --- p.113 / Chapter Chapter 7 --- General Discussion / Chapter 7.1 --- Advantages and weakness of DNA technology --- p.116 / Chapter 7.2 --- Choosing appropriate molecular markers --- p.118 / Chapter 7.3 --- Further suggested work --- p.119 / Chapter 7.4 --- Conclusion --- p.119 / References --- p.121 / Appendix --- p.130

La grande famille des facteurs de transcription Ets est caractérisée par un domaine de liaison à l’ADN, le domaine ETS, qui présente une structure de type hélice-tour-hélice ailé et qui reconnaît la séquence nucléotidique GGAA/T. Ces facteurs sont des protéines modulaires, dont les domaines sont structurellement conservés, régulent la transcription de leurs gènes cibles. L’action régulatrice de ces facteurs de transcription, ainsi que leur spécificité, dépendent de leurs sites d’expression, du taux auquel ils sont exprimés ainsi que des modifications post-traductionnelles qui les touchent. Au sein de la famille Ets, les trois membres du groupe PEA3 - Erm, Pea3 et Er81 - sont impliqués dans divers processus tant physiologiques tels que le développement des neurones sensitifs et moteurs que pathologiques tels que la croissance et l’invasion tumorale ou l’apparition de métastases, au niveau mammaire notamment.<p><p>Notre travail a eu pour ambition de mieux comprendre les relations structure/fonction des membres du groupe PEA3, et plus particulièrement de Erm. <p><p>\ / Doctorat en sciences biomédicales / info:eu-repo/semantics/nonPublished

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