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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
51

Identification of differentially expressed genes in fibroblasts from human hypertrophic scars by using differential display RT-PCR technique.

January 1998 (has links)
by Cheng Chi Wa. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 110-120). / Abstract also in Chinese. / Title --- p.i / Abstract --- p.ii / Acknowledgement --- p.iv / Abbreviations --- p.v / Abbreviation Table for Amino Acids --- p.vi / Table of Contents --- p.vii / List of Figures --- p.xii / List of Tables --- p.xv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter Chapter 2 --- Literature review --- p.2 / Chapter Part I --- Hypertrophic Scar / Chapter 2.1 --- Definition of hypertrophic scar --- p.2 / Chapter 2.2 --- Pathology --- p.2 / Chapter 2.3 --- Epidemiology findings --- p.3 / Chapter 2.3.1 --- Ethnicity --- p.3 / Chapter 2.3.2 --- Age --- p.3 / Chapter 2.3.3 --- Body location --- p.3 / Chapter 2.4 --- Mechanism of cutaneous wound healing --- p.4 / Chapter 2.4.1 --- Phase I - Haemostasis and inflammation --- p.4 / Chapter 2.4.1.1 --- Haemostasis --- p.6 / Chapter 2.4.1.2 --- Early phase of inflammation --- p.6 / Chapter 2.4.1.3 --- Late phase of inflammation --- p.7 / Chapter 2.4.2 --- Phase II - Re-epithelialization --- p.7 / Chapter 2.4.2.1 --- Migration of epidermal keratinocytes --- p.8 / Chapter 2.4.2.2 --- Migration of fibroblasts --- p.8 / Chapter 2.4.2.3 --- Angiogenesis --- p.9 / Chapter 2.4.3 --- Phase III - Tissue remodeling --- p.10 / Chapter 2.4.3.1 --- Cell maturation and apoptosis --- p.10 / Chapter 2.4.3.2 --- Exrtracellular matrix remodeling --- p.10 / Chapter 2.5 --- Alteration of wound healing - Possible pathogenic factors of hypertrophic scar --- p.11 / Chapter 2.5.1 --- Changes in Phase I-Inflammation --- p.13 / Chapter 2.5.2 --- Changes in Phase II - Re-epithelialization/ tissue formation --- p.14 / Chapter 2.5.3 --- Changes in Phase III - Tissue remodeling --- p.15 / Chapter 2.6 --- The Role of fibroblasts in the formation of hypertrophic scar --- p.16 / Chapter 2.6.1 --- Functions of fibroblasts in wound healing --- p.16 / Chapter 2.6.2 --- Suggested aetiological role in the formation of hypertrophic scar fibroblasts --- p.16 / Chapter 2.6.2.1 --- Fibroproliferation disorder --- p.18 / Chapter 2.6.2.2 --- Extracellular Matrix remodeling disorder --- p.18 / Chapter a) --- CoUaqen --- p.18 / Chapter b) --- Proteoglycan --- p.19 / Chapter 2.6.2.3 --- Other differentially expressed factors --- p.20 / Chapter 2.7 --- Treatment of hypertrophic scar --- p.21 / Chapter Part II --- Differential Display / Chapter 2.8 --- Current approaches for the studies of differential gene expression --- p.23 / Chapter 2.9 --- Comparison amongst different approaches --- p.23 / Chapter 2.10 --- The strategy of Differential Display RT-PCR (DDRT-PCR) --- p.24 / Chapter 2.11 --- The application of DDRT-PCR to identify differentially expressed genes --- p.26 / Chapter Chapter 3 --- Aims and Strategies --- p.27 / Chapter Chapter 4 --- Methods and Materials --- p.29 / Chapter 4.1 --- Materials --- p.29 / Chapter 4.2 --- Clinical specimen collection --- p.31 / Chapter 4.3 --- Primary explant culture --- p.31 / Chapter 4.4 --- Immunohistochemical staining --- p.32 / Chapter 4.5 --- Total RNA extraction --- p.32 / Chapter 4.6 --- DNase I digestion --- p.33 / Chapter 4.7 --- Differential display-RTPCR (DD-RTPCR) --- p.33 / Chapter 4.8 --- Polyacrylamide gel electrophoresis --- p.34 / Chapter 4.9 --- Reamplification of the differentially expressed fragments --- p.35 / Chapter 4.10 --- Molecular cloning of the DNA fragments --- p.35 / Chapter 4.11 --- Screening and miniprep of the plasmid DNA --- p.36 / Chapter 4.12 --- Cycle sequencing --- p.38 / Chapter 4.13 --- Data analysis --- p.38 / Chapter 4.14 --- RT-PCR --- p.39 / Chapter 4.15 --- Probe labeling by PCR with DIG-dUTP --- p.40 / Chapter 4.16 --- Southern blotting --- p.41 / Chapter Chapter5 --- p.42 / Chapter 5.1 --- Clinical Specimen --- p.42 / Chapter 5.2 --- Primary explant culture --- p.42 / Chapter 5.3 --- The total RNA extraction from the cultured fibroblast --- p.45 / Chapter 5.4 --- Differential display RT-PCR --- p.47 / Chapter 5.5 --- Reamplification of the DNA fragments --- p.49 / Chapter 5.6 --- Molecular cloning of the DNA fragment --- p.53 / Chapter 5.7 --- DNA sequencing of the inserts --- p.58 / Chapter 5.8 --- Analysis and identification of the DNA sequences --- p.62 / Chapter 5.9 --- Semi-quantitative RT-PCR analysis of the differentially expressed genes --- p.76 / Chapter Chapter6 --- p.87 / Chapter Part I --- Validity of the Findings / Chapter 6.1 --- The Limitation of Tissue Sampling --- p.87 / Chapter 6.2 --- Tissue Culture model --- p.88 / Chapter 6.3 --- Differential Display RT-PCR --- p.89 / Chapter 6.3.1 --- Identification of the differentially expressed genes --- p.89 / Chapter 6.3.2 --- Confirmation of the differentially expressed genes --- p.91 / Chapter 6.4 --- Technical difficulties and Limitations --- p.92 / Chapter 6.4.1 --- Sampling --- p.92 / Chapter 6.4.2 --- Primary tissue culture --- p.93 / Chapter Part II --- Significance and Future Studies / Chapter 6.5 --- Down-regulation of thrombospondin 1 (TSP 1) in the hypertrophic scar fibroblasts --- p.94 / Chapter 6.6 --- Biochemical and biological functions of TSP1 --- p.96 / Chapter 6.6.1 --- The biochemical functions of TSP1 --- p.96 / Chapter 6.6.2 --- The biochemical functions of TSP1 --- p.97 / Chapter 6.7 --- The role of TSP 1 in the pathogenesis of hypertrophic scar --- p.98 / Chapter 6.7.1 --- Down-regulation of TSP 1 may be responsible for the excessive microvessels in hypertrophic scar --- p.98 / Chapter 6.7.2 --- Down-regulation of TSP 1 may be responsible for the failure of the apoptosis of the fibroblasts in the hypertrophic scar --- p.101 / Chapter 6.8 --- Expression of TSP 1 during wound healing --- p.103 / Chapter 6.9 --- Expression of TSP 1 in hypertrophic scarring --- p.107 / Chapter 6.10 --- Cytochrome b561 and its biological function --- p.109 / Chapter 6.11 --- Future studies --- p.108 / Chapter 6.11.1 --- The expression of TSP 1 in hypertrophic scarring and normal wound healing --- p.108 / Chapter 6.11.2 --- The expression of cytochrome b561 --- p.109 / Chapter 6.11.3 --- A full scale study of differential display RT-PCR --- p.109 / References --- p.110 / Appendices --- p.121 / Chapter I --- The complete mRNA sequence of thrombospondin1 precursor --- p.121 / Chapter II --- The mRNA sequence of cytochrome b561 --- p.123
52

Identification of peroxisome proliferator response element (PPRE) in a novel peroxisome proliferator-activated receptor regulating gene, peroxisome proliferator and starvation-induced gene (PPSIG).

January 2006 (has links)
Ng Lui. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 243-257). / Abstracts in English and Chinese. / Abstract --- p.i_iii / Abstract (Chinese version) --- p.iv-v / Acknowledgements --- p.vi / Table of Contents --- p.vii-xvii / List of Abbreviations --- p.xviii-xx / List of Figures --- p.xxi-xxvi / List of Tables --- p.xxvii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Peroxisome Proliferators (PPs) --- p.1 / Chapter 1.2 --- Peroxisome proliferator-activated receptors (PPARs) --- p.3 / Chapter 1.2.1 --- What are PPARs? --- p.3 / Chapter 1.2.2 --- PPAR isoforms --- p.3 / Chapter 1.2.2.1 --- PPARp/δ --- p.3 / Chapter 1.2.2.2 --- PPARγ --- p.4 / Chapter 1.2.2.3 --- PPARα --- p.5 / Chapter 1.2.3 --- PPARα target genes --- p.5 / Chapter 1.2.3.1 --- Transcriptional regulation --- p.5 / Chapter 1.2.3.2 --- PPRE --- p.6 / Chapter 1.2.4 --- Physiological roles --- p.9 / Chapter 1.2.4.1 --- Lipid metabolism --- p.9 / Chapter 1.2.4.1.1 --- Cellular fatty acid uptake and fatty acid activation --- p.9 / Chapter 1.2.4.1.2 --- Intracellular fatty acid transport --- p.11 / Chapter 1.2.4.1.3 --- Mitochondrial fatty acid uptake --- p.12 / Chapter 1.2.4.1.4 --- Mitochondrial fatty-acid P-oxidation / Chapter 1.2.4.1.5 --- Peroxisomal fatty acid uptake --- p.13 / Chapter 1.2.4.1.6 --- Peroxisomal fatty acid oxidation --- p.13 / Chapter 1.2.4.1.7 --- Micorsomal co-hydroxylation of fatty acids --- p.14 / Chapter 1.2.4.1.8 --- Ketogenesis --- p.15 / Chapter 1.2.4.1.9 --- Bile acid metabolism --- p.15 / Chapter 1.2.4.1.10 --- Lipoprotein metabolism --- p.17 / Chapter 1.2.4.1.11 --- Hepatic lipogenesis --- p.18 / Chapter 1.2.4.2 --- Glucose metabolism --- p.19 / Chapter 1.2.4.2.1 --- Glycogenolysis --- p.19 / Chapter 1.2.4.2.2 --- Glycolysis --- p.20 / Chapter 1.2.4.2.3 --- Gluconeogenesis --- p.20 / Chapter 1.2.4.3 --- Urea cycle --- p.21 / Chapter 1.2.4.4 --- Biotransformation --- p.22 / Chapter 1.2.4.5 --- Inflammation --- p.23 / Chapter 1.2.4.6 --- Acute phase response --- p.23 / Chapter 1.2.5 --- Toxicological roles --- p.24 / Chapter 1.2.5.1 --- PPs induce hepatocarcinoma formation through PPARα --- p.24 / Chapter 1.2.5.2 --- Mechanism of PPARa-mediated PP-induced hepatocarcinoma --- p.25 / Chapter 1.2.5.2.1 --- Oxidative stress --- p.25 / Chapter 1.2.5.2.2 --- Hepatocellular proliferation and inhibition of apoptosis --- p.26 / Chapter 1.3 --- Discovery of novel PPARα target genes --- p.27 / Chapter 1.3.1 --- Peroxisome proliferator and starvation-induced gene (PPSIG) --- p.28 / Chapter 1.3.1.1 --- PPSIG is a putative PPARa target gene --- p.28 / Chapter 1.3.1.2 --- Examination of PPSIG FDD fragment cDNA sequence --- p.28 / Chapter 1.4 --- Objectives --- p.32 / Chapter Chapter 2 --- Materials and Methods --- p.38 / Chapter 2.1 --- Cloning of the full-length mouse PPSIG cDNA --- p.38 / Chapter 2.1.1 --- Rapid amplification of cDNA ends (RACE) --- p.38 / Chapter 2.1.1.1 --- Total RNA extraction --- p.38 / Chapter 2.1.1.1.1 --- Materials --- p.38 / Chapter 2.1.1.1.2 --- Methods --- p.38 / Chapter 2.1.1.2 --- Primers design --- p.39 / Chapter 2.1.1.3 --- 5' and 3' cDNA ends amplification --- p.42 / Chapter 2.1.1.3.1 --- Materials --- p.42 / Chapter 2.1.1.3.2 --- Methods --- p.42 / Chapter 2.1.2 --- Subcloning of 5' and 3'RACED products --- p.45 / Chapter 2.1.2.1 --- Ligation and transformation --- p.45 / Chapter 2.1.2.1.1 --- Materials --- p.45 / Chapter 2.1.2.1.2 --- Methods --- p.46 / Chapter 2.1.2.2 --- Screening of the recombinants --- p.48 / Chapter 2.1.2.2.1 --- PhenoI:chloroform test --- p.48 / Chapter 2.1.2.2.1.1 --- Materials --- p.48 / Chapter 2.1.2.2.1.2 --- Methods --- p.48 / Chapter 2.1.2.2.2 --- Restriction enzyme digestion --- p.48 / Chapter 2.1.2.2.2.1 --- Materials --- p.48 / Chapter 2.1.2.2.2.2 --- Methods --- p.49 / Chapter 2.1.3 --- DNA sequencing of the 5'and 3'RACED subclones --- p.49 / Chapter 2.1.4 --- Northern blot analysis using PPSIG 5' and 3' RACED cDNA as probes --- p.52 / Chapter 2.1.4.1 --- RNA sample preparation --- p.52 / Chapter 2.1.4.1.1 --- Materials --- p.52 / Chapter 2.1.4.1.2 --- Methods --- p.52 / Chapter 2.1.4.2 --- Formaldehyde-agarose gel electrophoresis and blotting of RNA --- p.52 / Chapter 2.1.4.2.1 --- Materials --- p.52 / Chapter 2.1.4.2.2 --- Methods --- p.53 / Chapter 2.1.4.3 --- Probe preparation --- p.55 / Chapter 2.1.4.3.1 --- DIG labeling of RNA probe from 5'RACED PPSIG cDN A subclone 5'#32 --- p.55 / Chapter 2.1.4.3.1.1 --- Materials --- p.55 / Chapter 2.1.4.3.1.2 --- Methods --- p.55 / Chapter 2.1.4.3.2 --- PCR DIG labeling of 3´ة RACED PPSIG cDNA subclone 3' #12 --- p.56 / Chapter 2.1.4.3.2.1 --- Materials --- p.56 / Chapter 2.1.4.3.2.2 --- Methods --- p.57 / Chapter 2.1.4.4 --- Hybridization --- p.57 / Chapter 2.1.4.4.1 --- Materials --- p.57 / Chapter 2.1.4.4.2 --- Methods --- p.57 / Chapter 2.1.4.5 --- Post-hybridization washing and colour development --- p.59 / Chapter 2.1.4.5.1 --- Materials --- p.59 / Chapter 2.1.4.5.2 --- Methods --- p.59 / Chapter 2.2 --- Cloning of the PPSIG genomic DNA --- p.61 / Chapter 2.2.1 --- Screening of bacterial artificial chromosome (BAC) clones --- p.61 / Chapter 2.2.1.1 --- Screening of a mouse genomic library --- p.61 / Chapter 2.2.1.2 --- "Purification of BAC DNA by solution I, II,III" --- p.61 / Chapter 2.2.1.2.1 --- Materials --- p.61 / Chapter 2.2.1.2.2 --- Methods --- p.61 / Chapter 2.2.2 --- Confirmation of PPSIG genomic BAC clones --- p.64 / Chapter 2.2.2.1 --- Genomic Southern blot analysis --- p.64 / Chapter 2.2.2.1.1 --- Agarose gel electrophoresis and blotting of BAC DNA --- p.64 / Chapter 2.2.2.1.1.1 --- Materials --- p.64 / Chapter 2.2.2.1.1.2 --- Methods --- p.64 / Chapter 2.2.2.1.2 --- DIG labeling of DNA probe by random priming --- p.65 / Chapter 2.2.2.1.2.1 --- Materials --- p.65 / Chapter 2.2.2.1.2.2 --- Methods --- p.65 / Chapter 2.2.2.1.3 --- Hybridization --- p.66 / Chapter 2.2.2.1.4 --- Post-hybridization washing and colour development --- p.66 / Chapter 2.2.2.2 --- EcoR I digestion --- p.67 / Chapter 2.2.2.2.1 --- Materials --- p.67 / Chapter 2.2.2.2.2 --- Methods --- p.67 / Chapter 2.2.2.3 --- Large scale preparation of BAC DNA --- p.67 / Chapter 2.2.2.3.1 --- Materials --- p.67 / Chapter 2.2.2.3.2 --- Methods --- p.68 / Chapter 2.2.3 --- Determination of PPSIG genomic sequences --- p.68 / Chapter 2.2.3.1 --- Primers design --- p.68 / Chapter 2.2.3.2 --- PCR --- p.73 / Chapter 2.2.3.2.1 --- Materials --- p.73 / Chapter 2.2.3.2.2 --- Methods --- p.73 / Chapter 2.2.3.3 --- Subcloning of the PPSIG genomic fragments --- p.73 / Chapter 2.2.3.3.1 --- Ligation and transformation --- p.73 / Chapter 2.2.3.3.2 --- PCR screening --- p.74 / Chapter 2.2.3.3.2.1 --- Materials --- p.74 / Chapter 2.2.3.3.2.2 --- Methods --- p.74 / Chapter 2.2.3.4 --- DNA sequencing --- p.75 / Chapter 2.3 --- Cloning of PPSIG-promoter reporter constructs --- p.75 / Chapter 2.3.1 --- Amplification of PPSIG 5'-flanking fragment by PCR --- p.75 / Chapter 2.3.1.1 --- Materials --- p.75 / Chapter 2.3.1.2 --- Methods --- p.75 / Chapter 2.3.2 --- Preparation of pGL3-Basic vector DNA --- p.81 / Chapter 2.3.2.1 --- Materials --- p.81 / Chapter 2.3.2.2 --- Methods --- p.81 / Chapter 2.3.3 --- Ligation and transformation --- p.84 / Chapter 2.3.3.1 --- Materials --- p.84 / Chapter 2.3.3.2 --- Methods --- p.84 / Chapter 2.3.4 --- Screening and confirmation of recombinants --- p.85 / Chapter 2.3.4.1 --- Materials --- p.85 / Chapter 2.3.4.2 --- Methods --- p.85 / Chapter 2.4 --- Cloning of PPSIG 5'-deletion promoter constructs --- p.87 / Chapter 2.4.1 --- Deletion of target fragments by restriction enzyme digestion --- p.87 / Chapter 2.4.1.1 --- Materials --- p.87 / Chapter 2.4.1.2 --- Methods --- p.88 / Chapter 2.4.2 --- Ligation and transformation --- p.90 / Chapter 2.4.2.1 --- Materials --- p.90 / Chapter 2.4.2.2 --- Methods --- p.90 / Chapter 2.4.3 --- Screening and confirmation of recombinants --- p.91 / Chapter 2.5 --- Cloning of PPSIG-PPRE reporter constructs --- p.91 / Chapter 2.5.1 --- Amplification of PPSIG-PPRE fragments --- p.91 / Chapter 2.5.1.1 --- Materials --- p.91 / Chapter 2.5.1.2 --- Methods --- p.93 / Chapter 2.5.2 --- Preparation of pGL3-Basic vector DNA --- p.96 / Chapter 2.5.2.1 --- Materials --- p.96 / Chapter 2.5.2.2 --- Methods --- p.96 / Chapter 2.5.3 --- Ligation and transformation --- p.97 / Chapter 2.5.3.1 --- Materials --- p.97 / Chapter 2.5.3.2 --- Methods --- p.97 / Chapter 2.5.4 --- Screening and confirmation of recombinants --- p.97 / Chapter 2.6 --- Cloning of PPSIG-PPRE deletion construct --- p.101 / Chapter 2.6.1 --- Deletion of PPRE fragment by Stu I/Xho I digestion --- p.101 / Chapter 2.6.1.1 --- Materials --- p.101 / Chapter 2.6.1.2 --- Methods --- p.101 / Chapter 2.6.2 --- "Ligation, transformation, screening and confirmation of recombinants" --- p.103 / Chapter 2.7 --- Construction of PPSIG-PPRE-deletion and PPSIG- PPRE-mutation constructs by site-directed mutagenesis --- p.105 / Chapter 2.7.1 --- Primers design --- p.105 / Chapter 2.7.2 --- Amplification of the left and right halves of the PPRE-deletion and PPRE-mutation constructs by PCR --- p.109 / Chapter 2.7.2.1 --- Materials --- p.109 / Chapter 2.7.2.2 --- Methods --- p.109 / Chapter 2.7.3 --- "Ligation, Dpn I digestion and transformation" --- p.110 / Chapter 2.7.3.1 --- Materials --- p.110 / Chapter 2.7.3.2 --- Methods --- p.110 / Chapter 2.7.4 --- Screening and confirmation of recombinants --- p.111 / Chapter 2.7.4.1 --- Materials --- p.111 / Chapter 2.7.4.2 --- Methods --- p.111 / Chapter 2.8 --- Cloning of mouse malonyl-CoA decarboxylase (MCD) and rat acyl-CoA binding protein (ACBP) PPRE reporter constructs --- p.112 / Chapter 2.8.1 --- Preparation of mouse and rat genomic DNA --- p.112 / Chapter 2.8.1.1 --- Materials --- p.112 / Chapter 2.8.1.2 --- Methods --- p.113 / Chapter 2.8.2 --- Amplification of MCD and ACBP PPRE fragments by PCR --- p.113 / Chapter 2.8.2.1 --- Materials --- p.113 / Chapter 2.8.2.2 --- Methods --- p.114 / Chapter 2.8.3 --- Ligation and transformation --- p.117 / Chapter 2.8.4 --- Screening and confirmation of recombinants --- p.117 / Chapter 2.9 --- Cloning of mPPARα and mRXRα expression plasmids --- p.119 / Chapter 2.9.1 --- RT-PCR of mouse PPARα and RXRa cDNAs --- p.119 / Chapter 2.9.1.1 --- Materials --- p.119 / Chapter 2.9.1.2 --- Methods --- p.119 / Chapter 2.9.2 --- Preparation of pSG5 vector DNA --- p.123 / Chapter 2.9.2.1 --- Materials --- p.123 / Chapter 2.9.2.2 --- Methods --- p.123 / Chapter 2.9.3 --- Ligation and transformation --- p.125 / Chapter 2.9.3.1 --- Materials --- p.125 / Chapter 2.9.3.2 --- Methods --- p.125 / Chapter 2.9.4 --- Screening and confirmation of recombinants --- p.125 / Chapter 2.9.4.1 --- Materials --- p.125 / Chapter 2.9.4.2 --- Methods --- p.126 / Chapter 2.10 --- Transient transfection and reporter assays --- p.128 / Chapter 2.10.1 --- Cell culture and transient transfection --- p.128 / Chapter 2.10.1.1 --- Materials --- p.128 / Chapter 2.10.1.2 --- Methods --- p.128 / Chapter 2.10.2 --- Assay for reporter construct luciferase activity --- p.131 / Chapter 2.10.2.1 --- Materials --- p.131 / Chapter 2.10.2.2 --- Methods --- p.131 / Chapter 2.11 --- Electrophoretic mobility-shift assay (EMSA) --- p.133 / Chapter 2.11.1 --- In vitro transcription/translation --- p.133 / Chapter 2.11.1.1 --- Materials --- p.133 / Chapter 2.11.1.2 --- Methods --- p.133 / Chapter 2.11.2 --- Preparation of AML-12 nuclear extract --- p.134 / Chapter 2.11.3 --- Preparation of DIG-labeled PPSIG-PPRE oligonucleotides --- p.136 / Chapter 2.11.3.1 --- Oligonucleotides design --- p.136 / Chapter 2.11.3.2 --- Annealing of single-stranded oligonucleotides to form double- stranded oligonucleotides --- p.136 / Chapter 2.11.3.2.1 --- Materials --- p.136 / Chapter 2.11.3.2.2 --- Methods --- p.138 / Chapter 2.11.3.3 --- 3' end labeling of the double-stranded oligonucleotides --- p.138 / Chapter 2.11.3.3.1 --- Materials --- p.138 / Chapter 2.11.3.3.2 --- Methods --- p.138 / Chapter 2.11.3.4 --- Testing the labeling efficiency of the double-stranded oligonucleoides --- p.139 / Chapter 2.11.3.4.1 --- Materials --- p.139 / Chapter 2.11.3.4.2 --- Methods --- p.139 / Chapter 2.11.4 --- Preparation of unlabeled oligonucleotides as competitors --- p.140 / Chapter 2.11.5 --- Binding reactions --- p.142 / Chapter 2.11.5.1 --- Perform with in vitro transcribed/translated proteins --- p.142 / Chapter 2.11.5.1.1 --- Materials --- p.142 / Chapter 2.11.5.1.2 --- Methods --- p.142 / Chapter 2.11.5.2 --- Perform with AML-12 nuclear extracts --- p.144 / Chapter 2.11.5.2.1 --- Materials --- p.144 / Chapter 2.11.5.2.2 --- Methods --- p.144 / Chapter 2.11.6 --- Detection of shift-up pattern --- p.145 / Chapter 2.11.6.1 --- Materials --- p.145 / Chapter 2.11.6.2 --- Methods --- p.145 / Chapter 2.12 --- Statistical analysis --- p.146 / Chapter Chapter 3 --- Results --- p.147 / Chapter 3.1 --- PPSIG cDNA sequence analysis --- p.147 / Chapter 3.1.1 --- Cloning of PPSIG full-length cDNA sequence --- p.147 / Chapter 3.1.2 --- Northern blot analysis of PPSIG --- p.160 / Chapter 3.1.3 --- "Comparison of PPSIG, Riken cDNA 0610039N19 and all-trans-13'14-dihydroretinol saturase cDNA sequences" --- p.163 / Chapter 3.2 --- PPSIG genomic sequence analysis --- p.166 / Chapter 3.2.1 --- Screening of the PPSIG BAC clone --- p.166 / Chapter 3.2.2 --- Cloning of PPSIG genomic fragments --- p.167 / Chapter 3.2.3 --- Examination of PPSIG genomic organization --- p.170 / Chapter 3.2.3.1 --- "Comparison of PPSIG, Riken cDNA 0610039N19 and all-trans-13'14-dihydroretinol saturase genomic sequence" --- p.177 / Chapter 3.3 --- Characterization of the 5'-flanking region of PPSIG --- p.184 / Chapter 3.4 --- Identification of a functional PPRE in the intron 1 of PPSIG gene --- p.201 / Chapter 3.5 --- Gel shift analysis of PPARa/RXRa heterodimer to PPSIG-PPRE --- p.222 / Chapter Chapter 4 --- Discussion --- p.234 / Chapter Chapter 5 --- Future studies --- p.241 / References --- p.243 / Appendix A Seating plan of transfection experiments (24-wells) / Chapter A1 --- Transfection experiment to study PPSIG-promoter reporter constructs --- p.258 / Chapter A2 --- Transfection experiment to study the PPSIG- promoter deletion constructs --- p.259 / Chapter A3 --- Transfection experiment to study the PPSIG-PPRE reporter constructs --- p.260 / Chapter A4 --- Transfection experiment to study PPSIG-PPRE- deletion and PPSIG-PPRE-mutation constructs --- p.262 / Appendix B Alignment result of RACE clone DNAs --- p.265 / Chapter B1 --- Alignment result of 5´ة#7 --- p.265 / Chapter B2 --- Alignment result of 5'#11 --- p.267 / Chapter B3 --- Alignment result of 5'#12 --- p.269 / Chapter B4 --- Alignment result of 5´ة#16 --- p.271 / Chapter B5 --- Alignment result of 5´ة#20 --- p.274 / Chapter B6 --- Alignment result of 5´ة#31 --- p.276 / Chapter B7 --- Alignment result of 5´ة#32 --- p.278 / Chapter B8 --- Consensus sequence of each 5'RACED clone --- p.280 / Chapter B9 --- Alignment result of all 5'RACE clones consensus sequence --- p.287 / Chapter B10 --- Alignment result of 3´ة#2 --- p.290 / Chapter B11 --- Alignment result of 3´ة#3 --- p.291 / Chapter B12 --- Alignment result of 3´ة#14 --- p.292 / Chapter B13 --- Alignment result of 3´ة#5 --- p.293 / Chapter B14 --- Alignment result of 3´ة#6 --- p.294 / Chapter B15 --- Alignment result of 3´ة#8 --- p.295 / Chapter B16 --- Alignment result of 3´ة#10 --- p.297 / Chapter B17 --- Alignment result of 3´ة#11 --- p.298 / Chapter B18 --- Alignment result of 3´ة#12 --- p.299 / Chapter B19 --- Alignment result of 3´ة#16 --- p.301 / Chapter B20 --- Alignment result of 3´ة#22 --- p.302 / Chapter B21 --- Alignment result of 3´ة#25 --- p.303 / Chapter B22 --- Consensus sequence of each 3'RACED clone --- p.305 / Chapter B23 --- Alignment result of all 3' RACE clones consensus sequence --- p.310 / Appendix C DNA sequencing and alignment result of PPSIG genomic fragments --- p.312 / Chapter C1 --- Exon 1 to exon 2 --- p.312 / Chapter C2 --- Exon 2 to exon 3 --- p.315 / Chapter C3 --- Exon 3 to exon 4 --- p.316 / Chapter C4 --- Exon 4 to exon 5 --- p.318 / Chapter C5 --- Exon 5 to exon 6 --- p.319 / Chapter C6 --- Exon 6 to exon 7 --- p.321 / Chapter C7 --- Exon 7 to exon 8 --- p.322 / Chapter C8 --- Exon 8 to exon 9 --- p.323 / Chapter C9 --- Exon 9 to exon 10 --- p.324 / Chapter C10 --- Exon 10 to exon 11 --- p.325 / Chapter C11 --- Exon 11 to downstream --- p.326 / Chapter C12 --- Consensus sequence of each BAC genomic DNA fragment --- p.328 / Chapter C13 --- The alignment result of all the PPSIG genomic sequence --- p.335 / Appendix D DNA sequencing and alignment result of constructs --- p.347 / Chapter D1 --- "pGL3-PPSIG (-2936/+119), pGL3-PPSIG (-1534/+119), pGL3-PPSIG (-879/+119) and pGL3- PPSIG (-375/+119) reporter constructs DNA sequencing and alignment result" --- p.347 / Chapter D2 --- pSG5-PPARa expression plasmid DNA sequencing and alignment result --- p.351 / Chapter D3 --- pSG5-RXRa expression plasmid DNA sequencing and alignment result --- p.353 / Chapter D4 --- pGL3-MCD reporter constructs DNA sequencing and alignment result --- p.355 / Chapter D5 --- pGL3-PPSIG (-229/+435) reporter construct DNA sequencing and alignment result --- p.356 / Chapter D6 --- pGL3-PPSIG (+94/+435) and pGL3-PPSIG (+94/+190) reporter constructs DNA sequencing and alignment result --- p.357 / Chapter D7 --- pGL3-PPSIG (-229/+3031) reporter construct DNA sequencing and alignment result --- p.358 / Chapter D8 --- pGL3-PPSIG (+94/+3031) reporter construct DNA sequencing and alignment result --- p.360 / Chapter D9 --- pGL3-ACBP reporter construct DNA sequencing and alignment result --- p.362 / Chapter D10 --- PPSIG-PPRE-deletion and PPSIG-PPRE-mutation constructs DNA sequencing and alignment result --- p.363
53

Investigation of the quantitative relationship between circulating placental mRNA and fetal growth.

January 2008 (has links)
Pang, Weng I. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 116-148). / Abstracts in English and Chinese. / ABSTRACT --- p.i / 摘要 --- p.iv / ACKNOWLEDGEMENTS --- p.vi / PUBLICATIONS --- p.vii / TABLE OF CONTENTS --- p.viii / LIST OF TABLES --- p.xiii / LIST OF FIGURES --- p.xv / LIST OF ABBREVIATIONS --- p.xvi / Chapter SECTION I: --- BACKGROUND --- p.1 / Chapter CHAPTER 1: --- CIRCULATING NUCLEIC ACIDS IN PRENATAL DIAGNOSIS --- p.2 / Chapter 1.1 --- Prenatal diagnosis --- p.2 / Chapter 1.2 --- Circulating fetal DNA in maternal plasma --- p.2 / Chapter 1.2.1 --- Biology of circulating fetal DNA --- p.2 / Chapter 1.2.2 --- Clinical applications of circulating fetal DNA --- p.3 / Chapter 1.2.2.1 --- Qualitative fetal-specific sequence detection --- p.4 / Chapter 1.2.2.2 --- Quantitative aberration detection --- p.4 / Chapter 1.2.3 --- Circulating fetal epigenetic markers --- p.5 / Chapter 1.3 --- Circulating fetal RNA in maternal plasma --- p.6 / Chapter 1.3.1 --- Biology of circulating fetal RNA --- p.6 / Chapter 1.3.2 --- Clinical applications of circulating fetal RNA --- p.8 / Chapter 1.3.2.1 --- Quantitative aberration detection --- p.8 / Chapter 1.3.2.2 --- Chromosomal aneuploidy detection --- p.9 / Chapter 1.3.3 --- Enrichment of fetal RNA --- p.10 / Chapter 1.4 --- Circulating microRNA in maternal plasma --- p.10 / Chapter CHAPTER 2: --- FETAL GROWTH AND WELL-BEING --- p.12 / Chapter 2.1 --- Normal fetal growth --- p.12 / Chapter 2.1.1 --- Role of the mother --- p.12 / Chapter 2.1.2 --- Role of the placenta --- p.12 / Chapter 2.1.3 --- Role of the fetus --- p.13 / Chapter 2.1.4 --- Role of the somatotrophic axis --- p.15 / Chapter 2.2 --- Abnormal fetal growth --- p.15 / Chapter 2.2.1 --- Intrauterine growth restriction --- p.16 / Chapter 2.1.2 --- Definition of IUGR --- p.16 / Chapter 2.2.3 --- Risk factors of IUGR --- p.17 / Chapter 2.2.4 --- Diagnosis of IUGR --- p.20 / Chapter 2.2.4.1 --- Biometric tests --- p.20 / Chapter 2.2.4.2 --- Biophysical tests --- p.21 / Chapter 2.2.4.3 --- Biochemical tests --- p.22 / Chapter 2.2.4.4 --- Others --- p.22 / Chapter 2.3 --- Limitations of current modalities in fetal growth assessment --- p.23 / Chapter 2.4 --- Aims of this thesis --- p.24 / Chapter SECTION II: --- MATERIALS AND METHODS --- p.26 / Chapter CHAPTER 3: --- QUANTITATIVE ANALYSIS OF CIRCULATING RNA --- p.27 / Chapter 3.1 --- Sample collection and processing --- p.27 / Chapter 3.1.1 --- Preparation of plasm a --- p.27 / Chapter 3.1.2 --- Preparation of blood cells --- p.27 / Chapter 3.1.3 --- Preparation of placental tissues --- p.27 / Chapter 3.2 --- Total RNA extraction --- p.28 / Chapter 3.2.1 --- Plasma and blood cells --- p.28 / Chapter 3.2.2 --- Placental tissues --- p.32 / Chapter 3.3 --- Quantitative measurements of nucleic acids --- p.32 / Chapter 3.3.1 --- Principles of real-time quantitative PCR --- p.33 / Chapter 3.3.2 --- One-step QR T-PCR assays for placental mRNA quantification --- p.3 7 / Chapter 3.3.3 --- QPCR assays for checking genomic DNA contamination --- p.43 / Chapter 3.4 --- Statistical analysis --- p.45 / Chapter SECTION III: --- EVALUATION OF PLACENTA-DERIVED MRNA AS POSSIBLE MARKERS FOR FETAL GROWTH ASSESSMENT --- p.46 / Chapter CHAPTER 4: --- SELECTION OF POTENTIAL FETAL GROWTH MRNA MARKERS FOR MATERNAL PLASMA DETECTION --- p.47 / Chapter 4.1 --- Introduction --- p.47 / Chapter 4.2 --- Materials and methods --- p.49 / Chapter 4.2.1 --- Sample collection and processing --- p.49 / Chapter 4.2.2 --- Experimental design --- p.49 / Chapter 4.2.3 --- RNA extraction and quantification --- p.51 / Chapter 4.2.4 --- Statistical analysis --- p.51 / Chapter 4.3 --- Results --- p.52 / Chapter 4.3.1 --- Identification of potential fetal growth mRNA markers in maternal plasma --- p.52 / Chapter 4.3.2 --- Development of real-time QR T-PCR assays --- p.56 / Chapter 4.3.3 --- Validation of maternal plasma detectability and pregnancy-specificity --- p.58 / Chapter 4.3.4 --- Assessment of the gestational trend in maternal plasma --- p.64 / Chapter 4.4 --- Discussion --- p.68 / Chapter CHAPTER 5: --- RELATIONSHIP BETWEEN CIRCULATING PLACENTAL MRNA AND FETAL GROWTH --- p.72 / Chapter 5.1 --- Introduction --- p.72 / Chapter 5.2 --- Materials and methods --- p.73 / Chapter 5.2.1 --- Sample collection and processing --- p.73 / Chapter 5.2.2 --- "Ultrasound measurement, placental weight and birth weight.…" --- p.74 / Chapter 5.2.3 --- Experimental design --- p.74 / Chapter 5.2.4 --- RNA extraction and quantification --- p.75 / Chapter 5.2.5 --- Statistical analysis --- p.75 / Chapter 5.3 --- Results --- p.75 / Chapter 5.3.1 --- Expression of potential growth markers in placental tissues --- p.76 / Chapter 5.3.2 --- Relationship between circulating placental mRNA and birth measurements --- p.76 / Chapter 5.3.3 --- Relationship between circulating placental mRNA and fetal biometric measurements --- p.77 / Chapter 5.4 --- Discussion --- p.85 / Chapter SECTION IV: --- CLINICAL APPLICATION OF POTENTIAL FETAL GROWTH MARKERS IN THE ASSESSMENT OF IUGR --- p.93 / Chapter CHAPTER 6: --- QUANTITATIVE ANALYSIS OF PLACENTAL MRNA IN IUGR WITH OR WITHOUT PET --- p.94 / Chapter 6.1 --- Introduction --- p.94 / Chapter 6.2 --- Materials and methods --- p.95 / Chapter 6.2.1 --- Sample collection and processing --- p.95 / Chapter 6.2.2 --- Experimental design --- p.96 / Chapter 6.2.3 --- RNA extraction and quantification --- p.96 / Chapter 6.2.4 --- Statistical analysis --- p.97 / Chapter 6.3 --- Results --- p.97 / Chapter 6.3.1 --- Cross-sectional comparison of placental mRNA concentrations --- p.97 / Chapter 6.3.2 --- Longitudinal comparison of placental mRNA concentrations --- p.102 / Chapter 6.4 --- Discussion --- p.103 / Chapter SECTION V: --- CONCLUDING REMARKS --- p.107 / Chapter CHAPTER 7: --- CONCLUSION AND FUTURE PERSPECTIVES --- p.108 / Chapter 7.1 --- A strategy for identifying circulating placental MRNA markers for fetal growth assessment --- p.108 / Chapter 7.2 --- Implications of mRNA marker development strategy --- p.111 / Chapter 7.3 --- Prospects for future work --- p.112 / REFERENCES --- p.116
54

Structure and function of the polypyrimidine region of the rat [alpha]1 (I) procollagen gene promoter /

Ririe, Seth S., January 2000 (has links)
Thesis (Ph. D.)--University of Missouri--Columbia, 2000. / "December 2000." Typescript. Vita. Includes bibliographical references (leaves 133-147). Also available on the Internet.
55

Mechanisms of factor recruitment at promoters during RNA polymerase II transcription /

Yudkovsky, Natalya. January 2001 (has links)
Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 72-93).
56

DNA microarray approaches to understanding the regulation and evolution of gene expression networks

Xue-Franzén, Yongtao, January 2009 (has links)
Diss. (sammanfattning) Stockholm : Karolinska institutet, 2009.
57

Gene complexes and regulatory domains in metazoan genomes /

Engström, Pär, January 2007 (has links)
Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 6 uppsatser.
58

DNA analogs for the purpose of gene therapy /

Svahn, Mathias G., January 2007 (has links)
Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.
59

Regulation of [beta]-catenin by Gli1 in epithelial transformation

Li, Xingnan. January 2006 (has links) (PDF)
Thesis (Ph. D.)--University of Alabama at Birmingham, 2006. / Title from first page of PDF file (viewed Oct. 31, 2007). Includes bibliographical references.
60

Characterization of chromatin dynamics during DNA repair and transcriptional regulation /

Tamburini, Beth Ann. January 2006 (has links)
Thesis (Ph.D. in Molecular Biology) -- University of Colorado at Denver and Health Sciences Center, 2006. / Typescript. Includes bibliographical references (leaves 137-151). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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