by Sik Lok Lam. / The "2" in the title is subscript. / Thesis (Ph.D.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 184-197). / ABSTRACT --- p.iii / ACKNOWLEDGEMENTS --- p.v / Chapter CHAPTER ONE: --- LITERATURE SURVEY OF SEQUENCE-SPECIFIC LOCAL STRUCTURAL VARIATIONS IN DEOXYRIBONUCLEIC ACID MOLECULES --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- General Review of DNA --- p.1 / Chapter 1.2.1 --- "Nomenclature, Symbols and Atomic Numbering Scheme of DNA" --- p.2 / Chapter 1.2.2 --- Conformations of DNAs --- p.6 / Chapter 1.2.3 --- Helix-to-Random-Coil Transition --- p.9 / Chapter 1.3 --- Sequence-Specific Local Structural Studies --- p.11 / Chapter 1.4 --- Purpose of This Work --- p.14 / Chapter CHAPTER TWO: --- DETERMINATION OF STRUCTURES OF SOLUTION DNA MOLECULES --- p.17 / Chapter 2.1 --- Introduction --- p.17 / Chapter 2.2 --- Optimization of Conditions --- p.17 / Chapter 2.3 --- Resonance Assignments --- p.19 / Chapter 2.4 --- Extraction of Structural Constraints --- p.22 / Chapter 2.4.1 --- Interproton Distances --- p.23 / Chapter 2.4.2 --- Endocyclic Sugar Torsion Angles --- p.25 / Chapter 2.4.3 --- Phosphate Backbone Torsion Angles --- p.29 / Chapter 2.4.4 --- Hydrogen Bonds --- p.31 / Chapter 2.5 --- Structural Refinement --- p.31 / Chapter CHAPTER THREE: --- SIGNIFICANCE OF DIFFERENT TYPES OF STRUCTURAL CONSTRAINTS IN STRUCTURAL REFINEMENT PROCESS --- p.35 / Chapter 3.1 --- Introduction --- p.35 / Chapter 3.2 --- Experimental --- p.36 / Chapter 3.2.1 --- DNA Model Building --- p.36 / Chapter 3.2.2 --- Generation of Structural Constraints --- p.37 / Chapter 3.2.3 --- Structural Refinement --- p.40 / Chapter 3.3 --- Results and Discussion --- p.41 / Chapter 3.3.1 --- Endocyclic Sugar Torsion Angle Constraints --- p.45 / Chapter 3.3.2 --- Phosphate Backbone Torsion Angle Constraints --- p.49 / Chapter 3.3.3 --- Hydrogen Bond Constraints --- p.50 / Chapter 3.4 --- Summary --- p.50 / Chapter CHAPTER FOUR: --- EFFECTS OF DIFFERENT VARIABLES IN THE RESTRAINED MOLECULAR DYNAMICS PROCESS --- p.52 / Chapter 4.1 --- Introduction --- p.52 / Chapter 4.2 --- Experimental --- p.53 / Chapter 4.3 --- Results and Discussion --- p.55 / Chapter 4.3.1 --- Variables in the Temperature Profile --- p.58 / Chapter 4.3.2 --- Variables in the Force Constant Profile --- p.62 / Chapter 4.4 --- Summary --- p.65 / Chapter CHAPTER FIVE: --- THE J-COUPLING RESTRAINED MOLECULAR MECHANICS PROTOCOL - AN EFFICIENT AND RELIABLE ALTERNATIVE IN DERIVING ENDOCYCLIC SUGAR TORSION ANGLE CONSTRAINTS --- p.66 / Chapter 5.1 --- Introduction --- p.66 / Chapter 5.2 --- Methodology --- p.71 / Chapter 5.2.1 --- "Establishment of the Correlation of 3J1'2, withvi" --- p.71 / Chapter 5.2.2 --- Sample Preparation --- p.73 / Chapter 5.2.3 --- NMR Analysis --- p.73 / Chapter 5.2.4 --- Theoretical Testing of the Protocol --- p.74 / Chapter 5.2.5 --- Experimental Testing of the Protocol --- p.75 / Chapter 5.3 --- Results and Discussion --- p.76 / Chapter 5.3.1 --- Selection of the Appropriate JrMM-derived Torsion Angles --- p.85 / Chapter 5.3.2 --- Theoretical Testing of the Protocol --- p.88 / Chapter 5.3.3 --- Experimental Testing of the Protocol --- p.93 / Chapter 5.4 --- Summary --- p.98 / Chapter CHAPTER SIX: --- HETERONUCLEAR SINGLE QUANTUM COHERENCE DERIVED BACKBONE TORSION ANGLE CONSTRAINTS --- p.99 / Chapter 6.1 --- Introduction --- p.99 / Chapter 6.2 --- Experimental --- p.102 / Chapter 6.3 --- Results and Discussion --- p.103 / Chapter 6.3.1 --- Determination of the Backbone Torsion Angles β and E --- p.103 / Chapter 6.3.2 --- Error Estimation on 3JC4'p- and 3JH3'p-derived E --- p.109 / Chapter 6.4 --- Summary --- p.110 / Chapter CHAPTER SEVEN: --- SOLUTION STRUCTURES OF d(CGXX，CG)2 AND d(CAXX´ةTG)2 --- p.111 / Chapter 7.1 --- Introduction --- p.111 / Chapter 7.2 --- Experimental --- p.111 / Chapter 7.2.1 --- Sample Preparation --- p.112 / Chapter 7.2.2 --- Resonance Assignment --- p.112 / Chapter 7.2.3 --- Melting Profile Study --- p.112 / Chapter 7.2.4 --- Extraction of Structural Constraints --- p.113 / Chapter 7.2.5 --- Structural Refinement --- p.115 / Chapter 7.2.6 --- Structural Parameter Analysis --- p.116 / Chapter 7.3 --- Results and Discussion --- p.116 / Chapter 7.3.1 --- Melting Profile Study --- p.117 / Chapter 7.3.2 --- Structural Constraints --- p.120 / Chapter 7.3.3 --- Structural Refinement --- p.129 / Chapter 7.3.4 --- Structural Features --- p.135 / Chapter CHAPTER EIGHT: --- SEQUENCE-SPECIFIC LOCAL STRUCTURAL STUDY --- p.156 / Chapter 8.1 --- Introduction --- p.156 / Chapter 8.2 --- Predictions from the Calladine's Rules --- p.156 / Chapter 8.3 --- Predictions from Olson's Base-Pair Morphology Dependent Clash Function --- p.160 / Chapter 8.4 --- Re-formulation of Calladine's Idea and its Relationship to Sequence-Specific Local Structural Function ΣLS --- p.163 / Chapter 8.4.1 --- Sequence-Specific Base-Pair Geometry Analysis --- p.164 / Chapter 8.4.2 --- Sequence-Specific Base-Pair Step Geometry Analysis --- p.166 / Chapter 8.4.3 --- Sequence-Specific Local Structural Function ΣLS --- p.167 / Chapter 8.5 --- Summary --- p.173 / Chapter CHAPTER NINE: --- CONCLUSIONS AND FURTHER WORK --- p.174 / APPENDIX I The Base Proton Regions of the lH NMR Spectra of the Hexamers --- p.177 / APPENDIX II 2D NOESY Spectra (Tm = 200 ms) of the Hexamers --- p.178 / "APPENDIX III The H1'-H27H2"" Regions of the DQF-COSY Spectra of the Hexamers" --- p.180 / APPENDIX IV The C4'-H4' Regions of the HSQC Spectra of the Hexamers --- p.182 / REFERENCES --- p.184

Thesis (Ph.D.)--University of Nevada, Reno, 2004. / Includes bibliographical references. Online version available on the World Wide Web.

by Yam Kwok Fai. / Year shown on spine: 1997. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 141-149). / Acknowledgments --- p.i / List of Contents --- p.ii / List of Figures --- p.viii / List of Tables --- p.xii / List of Primers --- p.xiii / Abbreviations --- p.xiv / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Growth Hormone (GH) --- p.1 / Chapter 1.2 --- Growth Hormone Receptor (GHR) --- p.3 / Chapter 1.2.1 --- Tissue Distribution of GHR --- p.4 / Chapter 1.2.2 --- Biosynthesis and Degradation of GHR --- p.6 / Chapter 1.2.3 --- Regulation of GHR Level --- p.7 / Chapter 1.2.4 --- The Structure of GHR --- p.9 / Chapter 1.2.5 --- The Structure of GHR Gene --- p.13 / Chapter 1.2.6 --- Growth Hormone Binding Protein (GHBP) --- p.14 / Chapter 1.2.7 --- The GH/Prolactin/Cytokine/Erythropoietin Receptor Superfamily --- p.15 / Chapter 1.2.8 --- Proposed Signal Transduction Pathway --- p.17 / Chapter 1.2.9 --- GHR Related Dwarfism --- p.22 / Chapter i). --- Substitution of certain amino acid residues in the extracellular domain --- p.22 / Chapter ii). --- Deletion of the extracellular domain --- p.23 / Chapter a). --- deletion of a small portion of the binding protein / Chapter b). --- deletion of a large portion of the binding protein / Chapter c). --- deletion of a large portion of the binding domain and the whole transmembrane domain / Chapter iii). --- Associated with normal GHBP --- p.24 / Chapter 1.3 --- Objectives of Cloning Vertebrate GHR cDNAs --- p.24 / Chapter Chapter 2 --- General Experimental Methods / Chapter 2.1 --- Preparation of Ribonuclease Free Reagents and Apparatus --- p.26 / Chapter 2.2 --- Isolation of Total RNA --- p.26 / Chapter 2.3 --- Isolation of mRNA --- p.26 / Chapter a). --- directly from tissue / Chapter b). --- from isolated total RNA / Chapter 2.4 --- Spectrophotometric Quantification and Qualification of DNA and RNA --- p.29 / Chapter 2.5 --- First Strand cDNA Synthesis --- p.29 / Chapter 2.6 --- Polymerase Chain Reaction (PCR) --- p.30 / Chapter 2.7 --- Agarose Gel Electrophoresis --- p.31 / Chapter 2.8 --- Formaldehyde Agarose Gel Electrophoresis of RNA --- p.31 / Chapter 2.9 --- Capillary Transfer of DNA/RNA to a Nylon Membrane (Southern/Northern Blotting) --- p.32 / Chapter a). --- DNA denaturing / Chapter b). --- Capillary transfer / Chapter 2.10 --- DNA Radiolabelling --- p.33 / Chapter a). --- By random primer translation / Chapter b). --- By nick translation / Chapter 2.11 --- Spuncolumn Chromatography --- p.34 / Chapter 2.12 --- Hybridization of Southern/Northern Blot --- p.35 / Chapter 2.13 --- Autoradiography --- p.35 / Chapter 2.14 --- Linearization and Dephosphorylation of Plasmid DNA --- p.36 / Chapter 2.15 --- Restriction Digestion of DNA --- p.36 / Chapter 2.16 --- Purification of DNA from Agarose Gel using GENECLEAN® Kit --- p.36 / Chapter 2.17 --- 3' End Modification of PCR Amplified DNA --- p.37 / Chapter 2.18 --- Ligation of DNA Fragments to Linearized Vector --- p.37 / Chapter 2.19 --- Preparation of Escherichia coli Competent Cells --- p.38 / Chapter 2.20 --- Transformation of the Escherichia coli Strain DH5a --- p.38 / Chapter 2.21 --- Minipreparation of Plasmid DNA --- p.39 / Chapter 2.22 --- DNA Purification by Phenol/Chloroform Extraction --- p.39 / Chapter 2.23 --- Ethanol Precipitation of DNA and RNA --- p.40 / Chapter 2.24 --- Preparation of Plasmid DNA using Wizard´ёØ Minipreps DNA Purification Kit from Promega --- p.40 / Chapter 2.25 --- Preparation of Plasmid DNA using QIAGEN-tip100 --- p.41 / Chapter 2.26 --- DNA Sequencing --- p.42 / Chapter 2.26.1 --- DNA Sequencing Reaction / Chapter a). --- T7 sequencing / Chapter b). --- PCR sequencing / Chapter 2.26.2 --- DNA Sequencing Electrophoresis --- p.44 / Chapter i). --- Preparation of 8% polyacrylamide gel solution / Chapter ii). --- Casting the gel / Chapter iii). --- Electrophoresis / Chapter Chapter 3 --- Molecular Cloning of Golden Hamster (Mesocricetus auratus) GHR cDNA / Chapter 3.1 --- Introduction --- p.46 / Chapter 3.2 --- Experimental Methods / Chapter 3.2.1 --- Animals and Tissues --- p.47 / Chapter 3.2.2 --- PCR Cloning of GHR cDNA Fragments in the Cytoplasmic Domain --- p.47 / Chapter 3.2.2.1 --- Primer design and PCR strategy --- p.47 / Chapter 3.2.2.2 --- PCR studies on the hamster liver and kidney first strand cDNA --- p.49 / Chapter 3.2.2.3 --- Southern analysis of the PCR products --- p.50 / Chapter 3.2.2.4 --- Subcloning and sequencing of PCR amplified cDNA fragments --- p.50 / Chapter 3.2.3 --- Screening of a Hamster Liver cDNA Library --- p.51 / Chapter 3.2.3.1 --- Preparation of the plating bacteria --- p.51 / Chapter 3.2.3.2 --- Phage titering of the λ ZAP library --- p.51 / Chapter 3.2.3.3 --- Primary screening of the amplified hamster liver cDNA library --- p.52 / Chapter 3.2.3.4 --- Plaque uplifting and hybridization with hamster GHR cDNA fragment --- p.52 / Chapter 3.2.3.5 --- Purification of putative clones from primary screening --- p.53 / Chapter 3.2.3.6 --- Checking the size of the DNA insert --- p.53 / Chapter 3.2.3.7 --- In vitro excision to release phagemid from the phage vector --- p.54 / Chapter 3.2.3.8 --- Plasmid minipreparation of the putative clones --- p.56 / Chapter 3.2.3.9 --- Nucleotide sequencing of the DNA inserts of different clones --- p.56 / Chapter 3.2.4 --- Tissue Distribution of GHR in Hamster Tissues and the Relative Expression Level of GHR mRNAin these tissues --- p.58 / Chapter 3.2.5 --- Cloning of the Full-length GHR cDNA into a Mammalian Vector --- p.59 / Chapter 3.2.5.1 --- PCR amplification of the full-length hamster GHR cDNA --- p.59 / Chapter 3.2.5.2 --- Preparation of the hamster GHR cDNA insert for ligation --- p.60 / Chapter 3.2.5.3 --- Linearization of pRc/CMV expression vector --- p.60 / Chapter 3.2.5.4 --- Ligation of the linearized expression vector with the full-length hamster GHR cDNA --- p.61 / Chapter 3.3 --- Results / Chapter 3.3.1 --- PCR Amplification of Hamster GHR cDNA Fragments --- p.61 / Chapter 3.3.1.1 --- RT-PCR --- p.61 / Chapter 3.3.1.2 --- Southern blot analysis --- p.62 / Chapter 3.3.1.3 --- Subcloning and nucleotide sequencing of PCR amplified hamster GHR cDNA fragments --- p.64 / Chapter 3.3.2 --- Screening of an Amplified λZAP Hamster Liver cDNA Library --- p.70 / Chapter 3.3.2.1 --- Preparation of the cDNA probe and phage titering --- p.70 / Chapter 3.3.2.2 --- Screening of the cDNA library --- p.70 / Chapter 3.3.2.3 --- PCR study of the 5' and 3' regions of the DNA insert of the clones selected for secondary screening --- p.72 / Chapter 3.2.3.4 --- Nucleotide sequencing of the full-length hamster GHR cDNA --- p.73 / Chapter 3.2.3.5 --- Tissue distribution of GHR in hamster and the relative expression level of the GHR mRNA in these tissues --- p.73 / Chapter 3.2.3.6 --- Cloning of the full-length hamster GHR cDNA into a mammalian expression vector --- p.79 / Chapter 3.4 --- Discussion / Chapter 3.4.1 --- Cloning of the Full-length hamster GHR cDNA --- p.81 / Chapter 3.4.2 --- Comparison of the Nucleotide and the Predicted Amino Acid Sequences of the Hamster GHR with other Cloned GHRs --- p.82 / Chapter 3.4.3 --- Tissue Distribution of GHR in Hamster and the Relative Expression Level of the GHR mRNA in these Tissues --- p.89 / Chapter 3.4.4 --- Further Studies on Hamster GHR --- p.90 / Chapter Chapter 4 --- Molecular Cloning of Chinese Bullfrog (Rana tigria rigulosa) GHR cDNA from Adult Frog Liver / Chapter 4.1 --- Introduction --- p.92 / Chapter 4.2 --- Experimental Methods / Chapter 4.2.1 --- Animal and Tissues --- p.93 / Chapter 4.2.2 --- Cloning of the Cytoplasmic Domain of Frog GHR cDNA by PCR --- p.93 / Chapter 4.2.2.1 --- RT-PCR --- p.93 / Chapter 4.2.2.2 --- Southern blot analysis of PCR amplified products --- p.95 / Chapter 4.2.2.3 --- Subcloning and sequencing of PCR amplified DNA fragments --- p.95 / Chapter 4.2.2.4 --- Restriction analysis of GHR cDNA fragment between GHR p1 and GHR p2 --- p.95 / Chapter 4.2.2.5 --- PCR cloning of other portions of frog GHR cDNA --- p.96 / Chapter 4.2.2.6 --- Subcloning and sequencing of PCR amplified GHR cDNA fragment using primers other than GHR p1 and GHR p2 --- p.97 / Chapter 4.3 --- Results / Chapter 4.3.1 --- Cloning of the Intracellular Domain of Frog GHR cDNA by RT-PCR --- p.97 / Chapter 4.3.1.1 --- RT-PCR --- p.97 / Chapter 4.3.1.2 --- Southern blot analysis --- p.98 / Chapter 4.3.1.3 --- Subcloning and sequencing of PCR amplified DNA fragments --- p.98 / Chapter 4.3.1.4 --- Restriction enzyme analysis of GHR cDNA fragments --- p.102 / Chapter 4.3.1.5 --- PCR cloning of other portions of frog GHR cDNA --- p.103 / Chapter 4.3.1.6 --- Subcloning and sequencing of PCR products from other portions of frog GHR cDNA --- p.103 / Chapter 4.4 --- Discussion / Chapter 4.4.1 --- Cloning of the Full-length frog GHR cDNA --- p.109 / Chapter 4.4.2 --- Further Studies on Frog GHR --- p.117 / Chapter Chapter 5 --- Attempts on the Molecular Cloning of Teleost GHR cDNA / Chapter 5.1 --- Introduction --- p.119 / Chapter 5.2 --- Experimental Methods / Chapter 5.2.1 --- Animals and Tissues --- p.120 / Chapter 5.2.2 --- PCR Cloning of Teleost GHR cDNA fragments --- p.120 / Chapter 5.2.2.1 --- Design of PCR primers --- p.120 / Chapter 5.2.2.2 --- Preparation of mRNA and synthesis of first strand cDNA --- p.122 / Chapter 5.2.2.3 --- PCR studies on dace and snakehead fish liver first strand cDNA --- p.122 / Chapter 5.2.2.3.1 --- PCR studies on dace liver first strand cDNA --- p.122 / Chapter 5.2.2.3.2 --- PCR studies on snakehead fish liver first strand cDNA --- p.122 / Chapter 5.2.3 --- "Northern Analysis on Dace, Snakehead fish and Eel mRNA" --- p.123 / Chapter 5.3 --- Results / Chapter 5.3.1 --- Molecular Studies on Dace GHR cDNA --- p.123 / Chapter 5.3.1.1 --- PCR studies on dace first strand cDNA --- p.123 / Chapter 5.3.2 --- PCR Studies on Teleost First Strand cDNA --- p.128 / Chapter 5.3.3 --- Northern Analysis on Teleost mRNA --- p.128 / Chapter 5.4 --- Discussion --- p.130 / Chapter 5.4.1 --- PCR Studies on Teleost GHR cDNA --- p.130 / Chapter 5.4.2 --- Northern Analysis on Teleost mRNA --- p.131 / Chapter Chapter 6 --- General Discussion / Chapter 6.1 --- Achievement of this Project --- p.134 / Chapter 6.1.1 --- Hamster GHR --- p.134 / Chapter 6.1.2 --- Frog GHR --- p.135 / Chapter 6.1.3 --- Teleost GHR --- p.136 / Chapter 6.2 --- Postulation on Cloned GHRs at the Molecular Level --- p.136 / Bibliography --- p.141 / Appendices --- p.150

Keung Yim Mei. / "October 2001." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (p. 187-195). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

by Lam Fung Ming. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 45-47). / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter CHAPTER 2 --- BACKGROUND --- p.4 / Section 2.1 DNA Cloning --- p.5 / Section 2.1.1 Principles of cell-based DNA cloning --- p.5 / Section 2.1.2. Polymerase Chain Reaction --- p.8 / Section 2.2 DNA Libraries --- p.10 / Section 2.3. Expressed Sequence Tags --- p.11 / "Section 2.4 dbEST - Database for ""Expressed Sequence Tag""" --- p.13 / Chapter CHAPTER 3 --- REDUCTION OF PARTIAL SEQUENCE REDUNDANCY AND CDNA ALIGNMENT --- p.15 / Section 3.1 Materials --- p.15 / Section 3.2 Our Algorithm --- p.16 / Section 3.3 Data Storage --- p.24 / Section 3.4 Criterion of Alignment --- p.27 / Section 3.5 Pairwise Alignment --- p.29 / Chapter CHAPTER 4 --- RESULTS AND DISCUSSION --- p.32 / Chapter CHAPTER 5 --- CONCLUSION AND FUTURE DEVELOPMENT --- p.42 / REFERENCES --- p.45 / APPENDIX --- p.i

Thesis (Ph. D.)--University of Alabama at Birmingham, 2006. / Title from first page of PDF file (viewed Feb 15, 2008). Includes bibliographical references.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 106-119).