Long Xiaohang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 132-155). / Abstracts in English and Chinese. / Thesis/Assessment Committee --- p.I / Statement from Author --- p.II / Acknowledgements --- p.III / Abstract --- p.V / 摘要 --- p.VII / Table of Contents --- p.IX / List of Tables --- p.XV / List of Figures --- p.XVI / List of Abbreviations --- p.XVIII / Chapter Chapter 1 --- General Introduction and Literature Review --- p.1 / Chapter 1.1 --- General introduction --- p.1 / Chapter 1.2 --- Literature review --- p.5 / Chapter 1.2.1 --- Rice --- p.5 / Chapter 1.2.1.1 --- Classification of rice --- p.5 / Chapter 1.2.1.2 --- Rice grain quality --- p.5 / Chapter 1.2.2 --- Overview of current information on the starch biosynthesis and regulation during seed development --- p.7 / Chapter 1.2.2.1 --- Starch property --- p.7 / Chapter 1.2.2.1.1 --- Structure of rice starch granules --- p.7 / Chapter 1.2.2.1.2 --- Properties of rice starch --- p.7 / Chapter 1.2.2.2 --- Starch synthesis related proteins --- p.8 / Chapter 1.2.2.2.1 --- The formation of ADP-glucose through AGPase --- p.10 / Chapter 1.2.2.2.2 --- The synthesis of starch by starch synthases --- p.10 / Chapter 1.2.2.2.2.1 --- Amylose biosynthesis --- p.10 / Chapter 1.2.2.2.2.2 --- Amylopectin biosynthesis --- p.11 / Chapter 1.2.2.2.3 --- Branching of the glucan chain by starch branching enzymes --- p.12 / Chapter 1.2.2.2.4 --- The role of debranching enzymes in polymer synthesis --- p.13 / Chapter 1.2.2.2.5 --- Starch degradation in plastids --- p.13 / Chapter 1.2.2.2.6 --- Other enzymes involved in starch synthesis pathway --- p.13 / Chapter 1.2.2.3 --- Starch biosynthesis regulation --- p.14 / Chapter 1.2.2.3.1 --- Developmental regulation --- p.14 / Chapter 1.2.2.3.2. --- Diurnal regulation --- p.15 / Chapter 1.2.2.3.3 --- 3-PGA/Pi regulation --- p.16 / Chapter 1.2.2.3.4. --- Sugar signaling --- p.17 / Chapter 1.2.2.3.5. --- Hormonal signaling --- p.18 / Chapter 1.2.2.3.6 --- Post translational modification regulation --- p.18 / Chapter 1.2.2.3.6.1 --- Post translational redox modulation --- p.18 / Chapter 1.2.2.3.6.2 --- Protein phosphorylation --- p.19 / Chapter 1.2.2.4 --- Rice grain quality improvement by genetic engineering --- p.20 / Chapter 1.2.2.4.1 --- Cooking and eating quality improvement --- p.20 / Chapter 1.2.2.4.1.1 --- Manipulation of starch content --- p.20 / Chapter 1.2.2.4.1.2 --- Manipulation of amylose/ amylopectin ratio --- p.20 / Chapter 1.2.2.4.2 --- Other targets for manipulating starch quality and quantity --- p.21 / Chapter 1.2.3 --- Proteomics --- p.23 / Chapter 1.2.3.1 --- General introduction --- p.23 / Chapter 1.2.3.2 --- Current technologies of proteomics --- p.25 / Chapter 1.2.3.2.1 --- Protein separation by 2D or non-2D method --- p.25 / Chapter 1.2.3.2.2 --- Protein visualization --- p.26 / Chapter 1.2.3.2.3 --- Computer-assisted image analysis --- p.27 / Chapter 1.2.3.2.4 --- Protein identification by mass spectrometry --- p.28 / Chapter 1.2.3.2.5 --- Database search --- p.28 / Chapter 1.2.3.2.5.1 --- Database searching software --- p.29 / Chapter 1.2.3.2.5.2 --- Protein sequence database --- p.29 / Chapter 1.2.3.2.5.3 --- Evaluating database hits --- p.30 / Chapter 1.2.3.2.6 --- Bioinformatics involved in proteomics --- p.31 / Chapter 1.2.3.2.7 --- Post translational modification --- p.32 / Chapter 1.2.3.2.7.1 --- Glycosylation --- p.32 / Chapter 1.2.3.2.7.1.1 --- N-linked glycosylation --- p.33 / Chapter 1.2.3.2.7.1.2 --- O-linked glycosylation --- p.33 / Chapter 1.2.3.2.7.2 --- Phosphorylation --- p.33 / Chapter 1.2.3.2.7.3 --- Strategies for studying PTMs --- p.34 / Chapter 1.2.3.2.8 --- Other aspects of proteomics --- p.36 / Chapter 1.2.3.2.8.1 --- 2D DIGE --- p.36 / Chapter 1.2.3.2.8.2 --- LC/LC-MS/MS --- p.36 / Chapter 1.2.3.2.8.2.1 --- MudPIT --- p.36 / Chapter 1.2.3.2.8.2.2 --- ICAT --- p.37 / Chapter 1.2.3.3 --- Plant proteomics --- p.37 / Chapter 1.2.3.3.1 --- Proteome analysis of plant tissues and organs --- p.38 / Chapter 1.2.3.3.2 --- Plant organelle proteomics --- p.39 / Chapter 1.2.3.3.3 --- Post translational modifications in plant --- p.41 / Chapter 1.2.3.4 --- Recent progress in rice proteomics --- p.42 / Chapter 1.2.3.4.1 --- General introduction of rice proteomics --- p.42 / Chapter 1.2.3.4.2 --- Rice proteome database construction --- p.43 / Chapter 1.2.3.4.3 --- Comparative proteomics --- p.43 / Chapter 1.2.3.4.4 --- Post translational modification study of rice proteome --- p.44 / Chapter Chapter 2 --- Materials and methods --- p.45 / Chapter 2.1 --- Materials --- p.45 / Chapter 2.1.1 --- Plant materials --- p.45 / Chapter 2.1.2 --- Chemical reagents and commercial kits --- p.46 / Chapter 2.1.3 --- Instruments --- p.46 / Chapter 2.1.4 --- Software --- p.46 / Chapter 2.2 --- Methods --- p.47 / Chapter 2.2.1 --- Fractionation of amyloplast and amyloplast membrane proteins --- p.47 / Chapter 2.2.2 --- Marker enzyme assays --- p.47 / Chapter 2.2.3 --- 2D gel electrophoresis --- p.48 / Chapter 2.2.4 --- Silver staining of 2D gel --- p.49 / Chapter 2.2.5 --- In-gel digestion of protein spots --- p.49 / Chapter 2.2.6 --- Desalination of the digested sample with ZipTip --- p.49 / Chapter 2.2.7 --- Protein identification by mass spectrometry and database searching --- p.50 / Chapter 2.2.8 --- Image and data analysis --- p.50 / Chapter 2.2.9 --- Extraction of starch granule associated proteins --- p.51 / Chapter 2.2.10 --- Western blot analysis --- p.51 / Chapter 2.2.11 --- Sample preparation for N terminal sequencing --- p.51 / Chapter 2.2.12 --- Phosphorylation and glycosylation assays --- p.52 / Chapter Chapter 3 --- Results --- p.53 / Chapter 3.1 --- Protein identification by ID and 2D PAGE --- p.53 / Chapter 3.1.1 --- Isolation and purification of amyloplasts from rice seeds --- p.53 / Chapter 3.1.2 --- Identification of amyloplast and amyloplast membrane proteins by MS/MS --- p.54 / Chapter 3.1.2.1 --- Sample preparation --- p.54 / Chapter 3.1.2.2 --- 2D and ID gel electrophoresis --- p.55 / Chapter 3.1.2.3 --- Protein identification by MS and MS/MS --- p.56 / Chapter 3.1.3 --- Functional classification of identified proteins --- p.69 / Chapter 3.1.3.1 --- Metabolism proteins --- p.71 / Chapter 3.1.3.2 --- Non starch synthesis metabolism proteins --- p.73 / Chapter 3.1.3.3 --- Protein destination --- p.73 / Chapter 3.1.3.4 --- Proteins with other functions --- p.74 / Chapter 3.1.4 --- Cross-correlation of experimental and calculated Mw of proteins --- p.74 / Chapter 3.1.5 --- Granule bound starch synthase (GBSS) --- p.75 / Chapter 3.1.5 --- N-terminal sequencing --- p.77 / Chapter 3.2 --- Protein profiling --- p.80 / Chapter 3.2.1 --- Seed collection and stages chosen --- p.80 / Chapter 3.2.2 --- The proteomic profiles of rice amyloplasts at different developing stages --- p.81 / Chapter 3.2.4 --- Comparing the proteome of three rice lines --- p.85 / Chapter 3.2.4.1 --- Spot number analysis --- p.85 / Chapter 3.2.4.2 --- Functional distribution analysis --- p.86 / Chapter 3.2.4.3 --- Protein amount analysis --- p.87 / Chapter 3.2.5 --- Comparison of expression pattern: cluster analysis (SOM) --- p.88 / Chapter 3.2.5.1 --- Cluster analysis of rice amyloplast proteome --- p.88 / Chapter 3.2.5.2 --- Three major categories of rice amyloplast proteome expression patterns --- p.91 / Chapter 3.2.6 --- Scatter plots analysis --- p.94 / Chapter 3.2.7 --- Comparison of changes in proteins related to starch synthesis --- p.96 / Chapter 3.2.7.1 --- GBSS --- p.96 / Chapter 3.2.7.2 --- AGPase --- p.98 / Chapter 3.2.7.3 --- SSS --- p.98 / Chapter 3.2.7.4 --- SBE --- p.98 / Chapter 3.2.7.5 --- SP --- p.98 / Chapter 3.3 --- Study on protein post translational modifications --- p.102 / Chapter 3.3.1 --- Post translational modifications that potentially regulate starch synthesis --- p.102 / Chapter 3.3.2 --- Post translational modifications at different developing stages --- p.104 / Chapter 3.3.2.1 --- Profiling of post translational modifications of rice amyloplast proteome --- p.104 / Chapter 3.3.2.2 --- Starch synthesis related proteins --- p.106 / Chapter 3.3.2.2.1 --- GBSS --- p.106 / Chapter 3.3.2.2.2 --- SSS --- p.108 / Chapter Chapter 4 --- Discussion --- p.111 / Chapter 4.1 --- Methodology --- p.111 / Chapter 4.1.1 --- Amyloplast isolation --- p.111 / Chapter 4.1.2 --- Protein extraction from amyloplasts --- p.111 / Chapter 4.1.3 --- Protein identification by PMF and MS/MS --- p.112 / Chapter 4.1.4 --- Methods used to study protein expression patterns --- p.113 / Chapter 4.1.5 --- New methods introduced to study post translational modifications --- p.114 / Chapter 4.2 --- Characteristics of rice amyloplast proteins --- p.115 / Chapter 4.2.1 --- Amyloplast proteins associated with starch granules --- p.116 / Chapter 4.2.2 --- Most proteins in amyloplast proteome contain the transit peptide --- p.116 / Chapter 4.2.3 --- Multiple isoforms of starch synthesis related proteins --- p.117 / Chapter 4.2.3.1 --- Multiple spots of GBSS --- p.118 / Chapter 4.2.4 --- Expression patterns of amyloplast proteome --- p.120 / Chapter 4.2.5 --- Post translational modifications potentially regulate starch synthesis --- p.122 / Chapter 4.3 --- Other characteristic aspects of amyloplast proteome --- p.123 / Chapter 4.3.1 --- Comparison between the rice and wheat amyloplast proteomes --- p.123 / Chapter 4.3.2 --- Proteomic comparisons among the three rice lines --- p.124 / Chapter 4.3.3 --- Comparison of starch synthesis enzymes at protein and transcript levels --- p.124 / Chapter 4.3.4 --- Comparison of the starch synthesis related proteins among the three rice lines --- p.126 / Chapter 4.4 --- Limitations of proteomic approach in directly answering the question on how to improve eating and cooling quality --- p.126 / Chapter Chapter 5 --- Conclusion --- p.128 / Chapter Chapter 6 --- Future perspectives --- p.130 / References --- p.132

Congenital Contractural Arachnodactyly (CCA), also known as Beal's syndrome, is an autosomal dominant disorder characterized by multiple congenital joint contractures, arachnodactyly, dolichostenomelia, and scoliosis with only rare ocular or cardiovascular involvement. CCA has been linked to the fibrillin-2 (FBN2) gene located on chromosome 5q23-31. The phenotype ofCCA is similar to Marfan syndrome (MFS) which is caused by defects in the fibrillin-1 (FBNl) gene located on chromosome 15. Fibrillin-1 and fibrillin-2 are components of extracellular matrix (ECM) elastic microfibrils. The linkage studies performed on families affected with CCA suggest that another gene in the area ofFBN2 could also be responsible for CCA. Microfibril associated protein-3 (MF AP-3), another microfibril protein gene, has been localized to chromosome 5q32-33.2, the region of FBN2. This study involves mutation analysis of five patients affected with CCA, three of whom are representative of families affected with CCA. Mutation analysis was performed by chemical mismatch cleavage (CMC) analysis and nonisotopic RNase cleavage assay (NIRCA) analysis on both FBN2 and MF AP-3 cDNA. Prior to this study only two mutations in FBN2 have been reported in two isolated patients with CCA and none have been reported for MFAP-3. The two mutations reported in FBN2 have not been confirmed in other affected family members. Mutation analysis by CMC completed in this study did not reveal any mutations in either FBN2 or MF AP-3. Reanalysis by NIRCA revealed two mutations in FBN2. One mutation which results in the skipping of exon 31 occurs in an intron and its location is presently unknown. The other mutation, a G to C transversion at nucleotide 3340, predicting a histidine substitution for an asparagine, is a mutation at the -1 position of the 5' splice site of an intron which results in partial exon skipping although it is unknown whether exon 25 or 26 is skipped. The missense mutation and partial exon skipping result in two different forms of mutant fibrillin-2 molecules. Both of the mutations are present in patients with additional affected family members. Characterization of these mutations will confirm the cosegregation of FBN2 mutations with the CCA phenotype.

Bibliography: leaves [127-137]

published_or_final_version / Pathology / Master / Master of Medical Sciences

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Pathology / Master / Master of Medical Sciences

published_or_final_version / Pathology / Master / Master of Medical Sciences

published_or_final_version / Clinical Oncology / Master / Master of Philosophy