Ulm, Univ., Diss., 2007.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2006. / Härtill 5 uppsatser.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2006. / Härtill 4 uppsatser.

Sonic Hedgehog (SHH) is a secreted morphogen that is an essential regulator of patterning and growth. The SHH protein requires cleavage of its full-length precursor (SHHFL) for secretion of biologically active SHH (SHHNp). Mutations in SHH that affect SHH processing are associated with human disease, which highlights the importance of processing for patterning in vivo. We identified Sortilin (SORT1), a member of the VPS10P receptor family, as a novel SHH interacting protein. SORT1 preferentially associates with SHHFL and SORT1 levels correlate inversely with cleavage of SHHFL. Consistent with an antagonistic relationship between SORT1 and SHH processing, loss of SORT1 results in an increase in SHH levels in axons and a partial rescue of Hedgehog-associated patterning defects in a mouse model of deficient SHH processing. Finally, we demonstrate a functional requirement for SORT1-mediated trafficking on SHH-dependent signaling from axons in the developing visual system in vivo. Our findings identify a novel role for SORT1 in the regulation of SHH processing and trafficking.

Innate immunity is the first line of defense against invading pathogens. It provides immediate protection by initiating both cellular and humoral immune reactions in response to a wide range of infections. It is also important to the development of long-lasting and pathogen-specific adaptive immunity. Thus, studying of the innate immunity, especially the pathogen recognition and signaling modulation, is crucial for understanding the intrinsic mechanisms underlying the host defense, as well as contributing the development of the fight against infectious diseases. Drosophila is an ideal model organism for study of innate immunity. Comparing to mammals, Drosophila immunity is relative conserved and less redundant. A variety of molecular and genetic tools available add further convenience to the research in this system. My work is focused on the signaling modulation by post-translational modification after activation. In these studies I demonstrated in the center of Imd pathway, the Imd protein undergoes proteolytic cleavage, K63-polyubiquitination, phosphorylation, K63-deubiquitination and K48-polyubiquitination/degradation in a stimulation-dependent manner. These modifications of Imd play a crucial role in regulating signaling in response to infection. The characterization of ubiquitin-editing event provides a new insight into the molecular mechanisms underlying the activation and termination of insect immune signaling pathway.

Diss. (sammanfattning) Umeå : Univ., 2004. / Härtill 4 uppsatser.

Thesis (Ph. D.)--Case Western Reserve University, 2005. / [School of Medicine] Department of Genetics. Includes bibliographical references. Available online via OhioLINK's ETD Center.

Thesis (Ph. D.)--University of Virginia, 2008. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a loss of voluntary movement over time, leading to paralysis and death. While 10% of ALS cases are inherited or familial (FALS), the majority of cases (90%) are sporadic (SALS) with unknown etiology. Approximately 20% of FALS cases are genetically linked to a mutation in the anti-oxidizing enzyme, superoxide dismutase (SOD1). SALS and FALS are clinically indistinguishable, suggesting a common pathogenic mechanism exists for both types. Since such a large number of genetic mutations in SOD1 result in FALS (>170), it is reasonable to suspect that non-genetic modifications to SOD1 induce structural perturbations that result in ALS pathology as well. In fact, misfolded SOD1 lacking any genetic mutation was identified in end stage spinal cord tissues of SALS patients using misfolded SOD1-specific antibodies. In addition, this misfolded WT SOD1 found in SALS tissue inhibits axonal transport in vitro, supporting the notion that misfolded WT SOD1 exhibits toxic properties like that of FALS-linked SOD1. Indeed, aberrant post-translational modifications, such as oxidation, cause WT SOD1 to mimic the toxic properties of FALS-linked mutant SOD1. Based on these data, I hypothesize that modified, misfolded forms of WT SOD1 contribute to SALS disease progression in a manner similar to FALS linked mutant SOD1 in FALS. The work presented in this dissertation supports this hypothesis. Specifically, one common misfolded form of SOD1 is defined and exposure of this toxic region is shown to enhance SOD1 toxicity. Preventing exposure, or perhaps stabilization, of this “toxic” region is a potential therapeutic target for a subset of both familial and sporadic ALS patients. Further, the possibility of exploiting this misfolded SOD1 species as a biomarker is explored. For example, an over-oxidized SOD1 species was identified in peripheral blood mononuclear cells (PBMCs) from SALS patients that is reduced in controls. Moreover, 2-dimensional gel electrophoresis revealed a more negatively charged species of SOD1 in PBMCs of healthy controls greatly reduced in SALS patients. This species is hypothesized to be involved in the degradation of SOD1, further implicating both misfolded SOD1 and altered protein homeostasis in ALS pathogenesis.

Ma Kit Wan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 189-206). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Table of Contents --- p.iii / Abstract --- p.xi / 摘要 --- p.xiv / Abbreviation List --- p.xv / List of Figures --- p.xvii / List of Tables --- p.xxiii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Ubiquitination --- p.1 / Chapter 1.1.1 --- Ubiquitin --- p.1 / Chapter 1.1.2 --- Ubiquitin Pathway --- p.3 / Chapter 1.1.3 --- Functions of Ubiquitination --- p.5 / Chapter 1.1.4 --- Ubiquitin Like Proteins --- p.8 / Chapter 1.2 --- SUMO Proteins --- p.10 / Chapter 1.2.1 --- SUMO Isoforms --- p.10 / Chapter 1.2.2 --- SUMO Structure --- p.11 / Chapter 1.3 --- Sumoylation --- p.14 / Chapter 1.3.1 --- Functions of Sumoylation --- p.14 / Chapter 1.3.1.1 --- General Functions of Sumoylation --- p.15 / Chapter 1.3.1.2 --- Function of Sumoylation on Transcription Factors / Chapter 1.3.1.3 --- Specific Function of SUMO-2/3 Conjugation / Chapter 1.3.2 --- Sumoylation Pathway --- p.19 / Chapter 1.4 --- E3 Ligases in Sumoylation --- p.24 / Chapter 1.4.1 --- Types and Functions of E3 Ligases --- p.23 / Chapter 1.4.2 --- Structure of PI AS --- p.23 / Chapter 1.4.3 --- Function of PI AS --- p.27 / Chapter 1.5 --- Aims of Study --- p.29 / Chapter Chapter 2 --- Materials & Methods --- p.30 / Chapter 2.1 --- Polymerase Chain Reaction (PCR) Screening of Multiple Human Tissue cDNA (MTC´ёØ) Panel --- p.30 / Chapter 2.1.1 --- Primer Design --- p.30 / Chapter 2.1.2 --- Semi-quantitative PCR --- p.31 / Chapter 2.1.2.1 --- Human MTC´ёØ Panel --- p.31 / Chapter 2.1.2.2 --- PCR --- p.32 / Chapter 2.2 --- DNA Cloning --- p.34 / Chapter 2.2.1 --- "Amplification of El, E3 (PIAS), PIAS1 Fragments" --- p.34 / Chapter 2.2.1.1 --- Primer Design --- p.34 / Chapter 2.2.1.2 --- PCR --- p.36 / Chapter 2.2.1.3 --- Purification of PCR Product --- p.37 / Chapter 2.2.2 --- Restriction Digestion --- p.37 / Chapter 2.2.3 --- Ligation --- p.40 / Chapter 2.2.4 --- Transformation --- p.40 / Chapter 2.2.4.1 --- Preparation of Chemically Competent Cells'(DH5α) --- p.40 / Chapter 2.2.4.2 --- Transformation of Ligation Product --- p.41 / Chapter 2.2.5 --- Plasmid Preparation --- p.42 / Chapter 2.2.6 --- Screening for Recombinant Clones --- p.43 / Chapter 2.2.7 --- Sequencing of Recombinant Plasmid --- p.43 / Chapter 2.3 --- Subcellular Localization Study --- p.45 / Chapter 2.3.1 --- Midi Scale Plasmid Preparation --- p.45 / Chapter 2.3.2 --- Transfection of GFP Recombinant Plasmids --- p.46 / Chapter 2.3.2.1 --- Cell Culture of WRL-68 & HepG2 Cell Lines --- p.46 / Chapter 2.3.2.2 --- LipofectAMINE Based Transfection --- p.47 / Chapter 2.3.3 --- Immunostaining of Endogenous SUMO-1 & -2/-3 --- p.48 / Chapter 2.3.4 --- Nucleus Staining by DAPI --- p.48 / Chapter 2.3.5 --- Fluorescent Microscopic Visualization --- p.49 / Chapter 2.3.6 --- Western Blotting --- p.49 / Chapter 2.3.6.1 --- LipofectAMINE Based Transfection --- p.49 / Chapter 2.3.6.2 --- Protein Extraction --- p.50 / Chapter 2.3.6.3 --- Protein Quantification --- p.51 / Chapter 2.3.6.4 --- SDS-PAGE Analysis --- p.51 / Chapter 2.3.6.5 --- GFP Fusion Proteins Detection --- p.52 / Chapter 2.4 --- Two-Dimensional Gel Electrophoretic Analyses --- p.54 / Chapter 2.4.1 --- Sample Preparation --- p.54 / Chapter 2.4.1.1 --- Protein Extraction from the Nucleus --- p.54 / Chapter 2.4.1.2 --- Clean Up of Extracted Nuclear Fraction --- p.55 / Chapter 2.4.2 --- First Dimensional Isoelectric Focusing (IEF) --- p.55 / Chapter 2.4.3 --- Second Dimension SDS-PAGE --- p.57 / Chapter 2.4.3.1 --- SDS-PAGE Analysis --- p.57 / Chapter 2.4.3.2 --- Silver Staining --- p.58 / Chapter 2.4.4 --- Image Analysis --- p.59 / Chapter 2.4.5 --- Protein Identification by Mass Spectrometry --- p.60 / Chapter 2.4.5.1 --- Sample Preparation --- p.60 / Chapter 2.4.5.2 --- Data Acquisition --- p.62 / Chapter 2.4.5.3 --- Data Analysis of Protein Fingerprinting --- p.62 / Chapter 2.5 --- Confirmation of the Differentially Expressed Proteins by RT-PCR & Western Blotting --- p.63 / Chapter 2.5.1 --- RT-PCR Analysis --- p.63 / Chapter 2.5.1.1 --- RNA Extraction --- p.63 / Chapter 2.5.1.2 --- First Strand cDNA Synthesis --- p.64 / Chapter 2.5.1.3 --- Normalization of cDNA Template --- p.64 / Chapter 2.5.1.4 --- PCR Amplification of the Target Genes --- p.65 / Chapter 2.5.2 --- Western Blotting --- p.66 / Chapter 2.6 --- Expression of Human PIAS and PIAS1 Fragments in Prokaryotic System --- p.67 / Chapter 2.6.1 --- Preparation of Competent Cells --- p.67 / Chapter 2.6.2 --- Small Scale Expression --- p.67 / Chapter 2.6.2.1 --- Transformation --- p.67 / Chapter 2.6.2.2 --- IPTG Induced Protein Expression --- p.68 / Chapter 2.6.3 --- Large Scale Expression of PIAS1 Fragments --- p.70 / Chapter 2.6.3.1 --- Transformation --- p.70 / Chapter 2.6.3.2 --- IPTG Induced Protein Expression --- p.70 / Chapter 2.6.4 --- Purification Trial of MBP-PIAS1-321-410 --- p.71 / Chapter 2.6.4.1 --- Binding of Amylose Resin & On Column Cleavage (with Low Concentration of DTT) --- p.71 / Chapter 2.6.4.2 --- Elution from the Amylose Resin & Cleavage (with Low Concentration of DTT) --- p.73 / Chapter 2.6.4.3 --- Elution from the Amylose Resin & Cleavage (with High Concentration of DTT) --- p.73 / Chapter 2.6.4.4 --- Purification of PIAS1-321-410 by Size ExclusionChromatography --- p.73 / Chapter 2.6.5 --- Purification of MBP-PIAS1 Fragments --- p.74 / Chapter 2.6.5.1 --- Purification by Affinity Column (Amylose) --- p.74 / Chapter 2.6.5.2 --- Amylose Resin Regeneration --- p.74 / Chapter 2.6.5.3 --- Purification by Both Affinity and Ion Exchange (Heparin) --- p.75 / Chapter 2.6.5.4 --- Regeneration of Heparin Column --- p.76 / Chapter 2.6.5.5 --- Purification by Size Exclusion Chromatography --- p.76 / Chapter 2.6.5.6 --- Regeneration of Size Exclusion Chromatography --- p.77 / Chapter 2.6.6 --- Co-expression & Purification of PIAS1 Fragment with E2 (Ubc9) --- p.77 / Chapter 2.6.6.1 --- Co-transformation of pMAL-PIASl (Fragments) & pET-Ubc9 --- p.77 / Chapter 2.6.6.2 --- Co-expression of PIAS1 Fragments & Ubc9 --- p.78 / Chapter 2.6.6.3 --- Purification by Affinity Column (Amylose Resin) --- p.78 / Chapter 2.6.6.4 --- Purification by Both Affinity & Ion Exchange (Heparin) --- p.79 / Chapter 2.6.6.5 --- Purification by Size Exclusion Chromatography --- p.79 / Chapter 2.6.7 --- Urea Treatment for the Purification of PIAS 1 Fragments --- p.80 / Chapter 2.6.7.1 --- Transformation --- p.80 / Chapter 2.6.7.2 --- IPTG Induced Protein Expression --- p.80 / Chapter 2.6.7.3 --- Purification by Affinity Column (Amylose Resin) --- p.80 / Chapter 2.6.7.4 --- Purification by Both Affinity & Ion Exchange (Heparin) --- p.80 / Chapter 2.6.7.5 --- Purification by Size Exclusion Chromatography --- p.81 / Chapter Chapter 3 --- Results --- p.82 / Chapter 3.1 --- Tissue Distribution of Human PIAS Genes --- p.82 / Chapter 3.1.1 --- Determination of the Number of Cycles for PCR --- p.82 / Chapter 3.1.2 --- General Expression Pattern of All PIAS Genes --- p.82 / Chapter 3.1.3 --- Tissue Distribution of PIAS1 --- p.83 / Chapter 3.1.4 --- Tissue Distribution of PIAS3 --- p.83 / Chapter 3.1.5 --- Tissue Distribution of PIASxa --- p.83 / Chapter 3.1.6 --- Tissue Distribution of PIASxp --- p.84 / Chapter 3.1.7 --- Tissue Distribution of PIASy --- p.84 / Chapter 3.2 --- Subcellular Localization of SUMO Pathway Components --- p.90 / Chapter 3.2.1 --- Overexpression Confirmation --- p.90 / Chapter 3.2.2 --- Multiple Bands Detected After Overexpression of EGFP- SUMO-1 --- p.91 / Chapter 3.2.3 --- Subcellular Localization of EGFP --- p.94 / Chapter 3.2.4 --- Subcellular Localization of El Subunits --- p.94 / Chapter 3.2.5 --- Subcellular Localization of E2 (Ubc9) --- p.95 / Chapter 3.2.6 --- Subcellular Localization of PIAS Proteins --- p.95 / Chapter 3.2.7 --- Subcellular Localization of PIAS1 Fragments --- p.96 / Chapter 3.2.8 --- Subcellular Localization of SUMO-1 --- p.97 / Chapter 3.3 --- Differential Protein Expression Pattern after Transient Transfection of SUMO-1 --- p.112 / Chapter 3.3.1 --- Protein Expression Profiles after Transient Transfection / Chapter 3.3.2 --- Identification of the Differential Expressed Proteins --- p.113 / Chapter 3.4 --- Confirmation of Differentially Expressed Proteins in Cells Overexpressing SUMO-1 --- p.124 / Chapter 3.4.1 --- RT-PCR Analyses --- p.124 / Chapter 3.4.1.1 --- Downregulation of RNA Transcript of hnRNP A2/B1 isoform B1 --- p.124 / Chapter 3.4.1.2 --- No Significant Change in the Transcription Level of UDG --- p.125 / Chapter 3.4.2 --- Western Blotting --- p.128 / Chapter 3.4.2.1 --- Upregulation of hnRNP A2/B1 at the Protein Level --- p.128 / Chapter 3.4.2.2 --- Different Molecular Weight of hnRNP A2/B1 Was Detected --- p.129 / Chapter 3.4.2.3 --- Upregulation of UDG at the Protein Level --- p.129 / Chapter 3.5 --- Expression & Purification of Human PIAS Proteins & PIAS1 Fragments --- p.133 / Chapter 3.5.1 --- Expression of Human PIAS Proteins --- p.133 / Chapter 3.5.2 --- Expression of PIAS1 Fragments --- p.135 / Chapter 3.5.3 --- A Trial of Purification of MBP-PIAS1-321-410 --- p.137 / Chapter 3.5.3.1 --- On Column Cleavage of MBP Tag --- p.137 / Chapter 3.5.3.2 --- Cleavage after Elution --- p.137 / Chapter 3.5.3.3 --- High Concentration of DTT Used --- p.138 / Chapter 3.5.3.4 --- Separation of the Cleaved and Non Cleaved Proteins --- p.138 / Chapter 3.5.4 --- Purification of the PIAS 1 Fragments --- p.141 / Chapter 3.5.4.1 --- Purified by Affinity Column (Amylose Resin) --- p.141 / Chapter 3.5.4.2 --- Purified by Heparin Column --- p.141 / Chapter 3.5.4.3 --- Purified by Gel Filtration --- p.143 / Chapter 3.5.5 --- Co-expression & Purification of PIAS1 Fragments & E2 --- p.147 / Chapter 3.5.5.1 --- Co-expression of PIAS1 Fragments & E2 --- p.147 / Chapter 3.5.5.2 --- Co-purification of PIAS1 Fragments & E2 Amylose --- p.147 / Chapter 3.5.5.3 --- Co-purification of PIAS1 Fragments & E2 by Heparin --- p.148 / Chapter 3.5.5.4 --- Co-purification of PIAS 1 Fragments with Ubc9 by Gel Filtration --- p.148 / Chapter 3.5.6 --- Urea Treatment for Purification of PIAS1 Fragments --- p.153 / Chapter 3.5.6.1 --- Purification by Amylose Resin --- p.153 / Chapter 3.5.6.2 --- Purification by Heparin --- p.153 / Chapter 3.5.6.3 --- Purification by Gel Filtration --- p.154 / Chapter Chapter 4 --- Discussion --- p.157 / Chapter 4.1 --- Tissue Specificity of PIAS Proteins --- p.157 / Chapter 4.1.1 --- Principle of Tissue Specificity Study --- p.157 / Chapter 4.1.2 --- Importance of Sumoylation --- p.158 / Chapter 4.1.3 --- Role of Sumoylation in Reproduction --- p.159 / Chapter 4.1.4 --- Functional Role of Sumoylation in Other Tissue --- p.160 / Chapter 4.2 --- Subcellular Localization of SUMO Pathway --- p.162 / Chapter 4.2.1 --- SUMO Conjugation Occurs in the Nucleus --- p.162 / Chapter 4.2.2 --- Does Sumoylation Occur Outside the Nucleus --- p.163 / Chapter 4.2.3 --- Dots-like Structure Formed by the PIAS --- p.164 / Chapter 4.2.4 --- SAP Domain and PINIT Motif Are Not Essential for Nuclear Targeting --- p.165 / Chapter 4.2.5 --- Signal Involves in the Formation of Nuclear Speckles --- p.167 / Chapter 4.3 --- Differentially Expressed Proteins under SUMO-1 Overexpression --- p.169 / Chapter 4.3.1 --- Increase in High Molecular Weight Proteins --- p.169 / Chapter 4.3.2 --- Upregulation of hnRNP A2/B1 & UDG in Protein Level --- p.170 / Chapter 4.3.3 --- Variants of hnRNP A2/B1 Formed --- p.172 / Chapter 4.3.4 --- Possibility of Sumoylation on hnRNP A2/B1 isoform B1 & UDG --- p.172 / Chapter 4.3.5 --- Possible Roles of SUMO-1 on hnRNP A2/B1 isoform B1 --- p.174 / Chapter 4.3.6 --- Mechanism of Sumoylation on mRNA Processing --- p.175 / Chapter 4.3.7 --- Possible Roles of SUMO-1 on UDG --- p.176 / Chapter 4.3.8 --- Important of SUMO on Genome Integrity --- p.178 / Chapter 4.3.9 --- Sumoylation and Carcinogenesis --- p.178 / Chapter 4.4 --- Protein Purification of the Human PIAS Proteins & PIAS1 Fragments --- p.180 / Chapter 4.4.1 --- Low Expression Level & Solubility of the PIAS Proteins --- p.180 / Chapter 4.4.2 --- High Expression Level & Solubility of PIAS 1 Fragments --- p.181 / Chapter 4.4.3 --- Incorrect Disulfide Bond Formation of the PIAS1 Fragments --- p.182 / Chapter 4.4.4 --- MBP-PIAS1 Fragments Formed Soluble Aggregates --- p.182 / Chapter 4.4.5 --- A Low Concentration of Urea Cannot Dissociate the Soluble Aggregates --- p.183 / Chapter 4.4.6 --- Aggregation May Weaken the Interaction between the PIAS1 Fragments & Ubc9 --- p.184 / Chapter 4.5 --- Conclusion --- p.185 / Chapter 4.6 --- Future Perspectives --- p.187 / Chapter 4.6.1 --- Identification of the Role of SUMO Interacting Motif in the Nuclear Speckle Formation --- p.187 / Chapter 4.6.2 --- Investigation of Sumoylation on Liver Cancer --- p.187 / Chapter 4.6.3 --- Optimization of the Expression & Purification of the PIAS Proteins --- p.188 / References --- p.189 / Appendix --- p.207