Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Please read the abstract in the section 00front of this document / Thesis (PhD (Microbiology))--University of Pretoria, 2005. / Microbiology and Plant Pathology / unrestricted

The poultry-to-human transmission of the influenza virus and the recent H1Nl influenza pandemic have become major concerns worldwide. The nucleoprotein (NP) of influenza virus binds the RNA genome and plays essential role in transcription and replication during the virus life cycle. / The study leads to a better understanding towards the RNP organization of influenza virus and provides information for the future design of anti-influenza agents. / We have also shown, by RNP reconstitution assay and co-immunoprecipitation, that the interaction between NP and PB2 is crucial for the proper functioning of the RNP. The functional association of NP and PB2 requires either the PB2 host-determining residue lysine-627 or arginine-630 with the latter involving NP arginine-150 also. Using SPR, we have demonstrated that both residues take part in the direct protein-protein interaction, without the involvement of RNA. These results suggest a dual interaction mechanism between NP and PB2. This may confer replication advantages to the virus, as either one can give an active RNP and explains the increased virulence of avian influenza viruses carrying the E627K mutation in mammalian cells. In addition, our findings identify the NP-PB2 interacting surface, with the PB2 627/630 region facing the RNA binding groove of NP. / We have determined the 3.3 A crystal structure of H5N1 NP, which is composed of head and body domains and a tail loop. Using surface plasmon resonance (SPR), we found the basic loop (residues 73-91) and arginine-rich groove, but mostly a protruding element centering at R174 and R175, to be important in RNA binding. Ribonucleoprotein (RNP) reconstitution assay with these multiple-point and deletion mutants indicate their functional importance towards the transcription-replication activities of the virus polymerase. Single-point mutations at these concerned regions do not have a significant effect on their RNP activities, suggesting that NP mediates RNA-binding through multiple residues. / Ng, Ka Leung. / Adviser: Pang Chui Shaw. / Source: Dissertation Abstracts International, Volume: 73-06, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 121-136). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Chan, Wai Hon. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 134-141). / Abstracts in English and Chinese. / Acknowledgements --- p.2 / Abstract --- p.3 / 摘要 --- p.5 / Content --- p.6 / List of Abbreviations and symbols --- p.10 / Chapter Chapter 1 --- Introduction --- p.13 / Chapter 1.1 --- The Severity of Influenza A Virus --- p.14 / Chapter 1.2 --- Introduction to Influenza A Virus --- p.15 / Chapter 1.3 --- What is Nucleoprotein? --- p.17 / Chapter 1.4 --- Multifunctional role of Nucleoprotein --- p.19 / Chapter 1.4.1 --- Interaction of Nucleoprotein with Other Viral Components --- p.19 / Chapter 1.4.1 --- Interaction of Nucleoprotein with Cellular Components --- p.22 / Chapter 1.5 --- Aims of study --- p.23 / Chapter Chapter 2 --- Materials and Methods / Chapter 2.1 --- Materials --- p.25 / Chapter 2.1.1 --- Chemical reagents --- p.25 / Chapter 2.1.2 --- Buffers --- p.28 / Chapter 2.1.2.1 --- Preparation of Buffers --- p.28 / Chapter 2.1.2.2 --- Buffer for Common Use --- p.28 / Chapter 2.1.3 --- Plasmids and Strains --- p.31 / Chapter 2.2 --- Methods --- p.32 / Chapter 2.2.1 --- Molecular Cloning --- p.32 / Chapter 2.2.2 --- "Expression of the Recombinant NP-WT/ mutants and importin α1, 3and 5 in E.coli" --- p.46 / Chapter 2.2.3 --- Purification of the NP WT/ variants --- p.50 / Chapter 2.2.4 --- "Purification of importin αl, 3 and 5" --- p.53 / Chapter 2.2.5 --- In vitro interaction study between NP and importin α --- p.56 / Chapter 2.2.6 --- In vivo interaction study between NP and importin α --- p.59 / Chapter 2.2.7 --- In vivo analysis to study NP-NP homo-oligomerization --- p.64 / Chapter 2.2.8 --- In vitro static light scattering analysis to determine NP oligomeric state --- p.68 / Chapter 2.2.9 --- Control experiments to verify NP-polymerases and NP-RNA interaction --- p.69 / Chapter Chapter 3 --- Functional analysis of influenza H5N1 nucleoprotein tail loop for oligomerization and ribonucleoprotein activities / Chapter 3.1 --- Introduction --- p.72 / Chapter 3.2 --- Results --- p.75 / Chapter 3.2.1 --- Tail loop insertion is maintained by intra- and inter-molecular interactions --- p.75 / Chapter 3.2.2 --- NP mutants display defective transcription-replication activity --- p.77 / Chapter 3.2.3 --- Expression and purification of defective NP variants --- p.80 / Chapter 3.2.4 --- Defective NP variants interact with RNA and the polymerase complex --- p.85 / Chapter 3.2.5 --- Defective NP variants possess abnormal oligomeric states in vitro --- p.91 / Chapter 3.2.6 --- NP variants with impaired RNP activity cannot form homo-oligomers in vivo --- p.95 / Chapter 3.3 --- Discussion --- p.98 / Chapter Chapter 4 --- Biophysical characterization of the interaction between influenza nucleoprotein and importin α / Chapter 4.1 --- Introduction --- p.105 / Chapter 4.2 --- Results --- p.108 / Chapter 4.2.1 --- Expression and Purification of NP-WT/ NLS variants and Importin a --- p.108 / Chapter 4.2.2 --- Pull down Assay --- p.113 / Chapter 4.2.3 --- Light scattering analysis (NP-lmportin α5) --- p.114 / Chapter 4.2.4 --- Binding assay of NP NLS variants with importin α5 --- p.115 / Chapter 4.2.5 --- BIAcore 3000 Surface Plasmon Resonance (NP-lmportin α5) --- p.118 / Chapter 4.2.6 --- QRT-PCR (NP-lmportin a5) --- p.123 / Chapter 4.3 --- Discussion --- p.125 / References --- p.134

published_or_final_version / abstract / Paediatrics and Adolescent Medicine / Doctoral / Doctor of Philosophy

Acute Myeloid Leukemia (AML), the most common form of acute leukemia in adults, is only curable in approximately 30% of all cases. Despite prognostic risk stratification using sub-typing and cytogenetic analysis to direct therapy, the mortality and relapse rate remains high. AML patients with normal karyotypes are defined as intermediate risk and are the most challenging to treat. Somatic mutations may be the key in refining prognostic stratification and providing useful therapeutic targets. The FMS-like tyrosine kinase 3 (FLT3) and Nucleophosmin (NPM1) genes have common mutated forms that are associated with overall survival and response to therapy. We assessed mutations in the FLT3 and NPM1 genes and their levels of expression in twenty eight AML patients in the presence and absence of HIV and their response to induction therapy. Furthermore, we used a novel technique, High Resolution Melting (HRM) Analysis to detect FLT3 Internal Tandem Duplications (ITD) and NPM1 exon 12 mutations. Five of the patients in this study were HIV positive, three of whom did not survive post-induction therapy. Of the AML patients, 17.9% were positive for the NPM1 mutation and 21% had mutated FLT3. Interestingly, the presence of the FLT3 and NPM1 mutations were coupled with an increase in expression levels of FLT3 and NPM1 from presentation to post-induction respectively and the loss of these mutations were coupled with a decrease in levels of expression from presentation to post-induction. However, an increase/decrease from presentation to post-induction did not necessarily denote the presence/absence of a mutation. Therefore, while mutational status of genes may generally confer mRNA levels, our results showed that there existed no definitive trend between mRNA levels of NPM1 and FLT3 expression and mutational status. We found that the HRM method was definitive for the simpler NPM1 mutation however detection of the FLT3-ITD mutation was challenging. There isn’t a clear distinction between mutated and non-mutated FLT3 due to the formation of hetero-duplexes during analysis, making detection highly subjective and error-prone. Sequencing allowed confirmation of mutated FLT3 and non-mutated FLT3 which were not in all instances in concordance with HRM analysis. The prognostic value in terms of overall survival of NPM1 and FLT3 mutations in this study is indefinite. Furthermore, the analysis of the HIV positive AML patients revealed no clear correlation between NPM1 and FLT3 levels of mRNA expression and mutational status. Also, the small number of HIV positive AML patients did not allow for conclusions to be made regarding HIV status and survival when affected with AML. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

by Chan Po-cheung. / Thesis (Ph.D.)--Chinese University of Hong Kong, 1994. / Includes bibliographical references (leaves 218-244). / Acknowledgement --- p.i / Abbreviations --- p.ii / Abstract --- p.iv / Table of content --- p.ix / Chapter Chapter 1. --- Biochemistry of Tumor Necrosis Factor --- p.1 / Chapter I. --- Introduction --- p.1 / Chapter 1.1 --- The discovery of tumor necrosis factor (TNF) --- p.1 / Chapter 1.2 --- TNF as an antitumor agent --- p.3 / Chapter 1.3 --- Production of TNF --- p.4 / Chapter 1.4 --- Structure of TNF --- p.5 / Chapter 1.5 --- TNF receptor --- p.6 / Chapter 1.6 --- Biological activities of TNF --- p.10 / Chapter 1.7 --- Anti-tumor activity of TNF --- p.14 / Chapter 1.7.1 --- In vitro studies --- p.14 / Chapter 1.7.1.1 --- Synergistic effect of other cytokines --- p.14 / Chapter 1.7.1.2 --- DNA damages --- p.15 / Chapter 1.7.1.3 --- Free radical generation --- p.15 / Chapter 1.7.1.4 --- Utilization of ATP --- p.16 / Chapter 1.7.1.5 --- Phospholipase A2 activation --- p.17 / Chapter 1.7.2 --- In vivo studies --- p.17 / Chapter 1.8 --- Clinical trials --- p.18 / Chapter Chapter 2. --- Materials and Methods --- p.20 / Chapter 2.1 --- Materials --- p.20 / Chapter 2.2 --- Solutions commonly used --- p.21 / Chapter 2.3 --- Methods and procedure --- p.23 / Chapter 2.3.1 --- Culture of L-929 cells --- p.23 / Chapter 2.3.2 --- Trypan Blue exclusion test --- p.23 / Chapter 2.3.3 --- Determination of viability of L-929 cells upon rhTNF treatment --- p.24 / Chapter 2.3.4 --- Determination of cellular cAMP level --- p.25 / Chapter 2.3.5 --- Determination of inositol phosphate turnover --- p.26 / Chapter 2.3.6 --- Use of fluorescence probe in the study of rhTNF mediated killing --- p.28 / Chapter 2.3.6.1 --- Determination of changes in internal pH of L-929 cells --- p.29 / Chapter 2.3.6.2 --- Determination of intracellular calcium level in L-929 cells --- p.30 / Chapter 2.3.6.3 --- Determination of membrane potential by fluorescence probes --- p.32 / Chapter 2.3.6.4 --- "Translocation of nucleolar protein, nucleophosmin (B23)in L-929 cells" --- p.32 / Chapter 2.3.6.5 --- Determination of calcium mobilization in L-929 cells by confocal microscopy --- p.34 / Chapter 2.3.6.6 --- Determination of protein kinase C and phospho-tyrosine kinase in L-929 cells --- p.34 / Chapter 2.3.7 --- Uptake of 45Ca2+ in L-929 cells --- p.35 / Chapter 2.3.8 --- Measurement of membrane potential by Patch-clamp assay --- p.36 / Chapter 2.3.9 --- Determination of tyrosine kinase activation by Western blotting --- p.36 / Chapter 2.3.10 --- Statistical analysis --- p.38 / Chapter Chanter 3. --- Effect of rhTNF treatment on nucleophosmin in L-929 cells --- p.39 / Chapter 3.1 --- Introduction --- p.39 / Chapter 3.2 --- Results --- p.43 / Chapter 3.2.1 --- Effect of TNF (in the presence or absence of actinomycin D) on the nucleophosmin translocation in L-929 cells --- p.43 / Chapter 3.2.2 --- Effect of actinomycin D on the TNF-mediated cytotoxicity on L-929 cells --- p.51 / Chapter 3.3 --- Discussion --- p.57 / Chapter Chapter 4. --- Changes in membrane potential and intracellular pH in rhTNF-mediated cytotoxicity in L-929 cells --- p.59 / Chapter 4.1 --- Introduction --- p.59 / Chapter 4.2 --- Results --- p.61 / Chapter 4.2.1 --- Effect of rhTNF on the membrane potential of L-929 cells determined by fluorescence method --- p.61 / Chapter 4.2.2 --- Effect of rhTNF on the membrane potential of L-929 cells determined by patch clamp technique --- p.64 / Chapter 4.2.3 --- "Effect of K+, Na+ and pH on the rhTNF-mediated cytotoxicity on L-929 cells" --- p.67 / Chapter 4.3 --- Discussion --- p.90 / Chapter Chapter 5. --- Effect of intracellular cAMP and cAMP-dependent protein kinase (PKA) on the rhTNF-mediated cytotoxicity on L-929 cells --- p.92 / Chapter 5.1 --- Introduction --- p.92 / Chapter 5.1.1 --- "GTP-binding protein (G protein), cAMP and protein kinase A" --- p.92 / Chapter 2.1.2 --- Role of cAMP as second messenger --- p.96 / Chapter 5.1.3 --- Bacterial toxin used for study of G-protein --- p.98 / Chapter 5.1.4 --- Effect of cAMP on rhTNF cytotoxicity --- p.99 / Chapter 5.1.5 --- Effect of cAMP-dependent protein kinase (PICA) on rhTNF cytotoxicity --- p.101 / Chapter 5.2 --- Results --- p.102 / Chapter 5.2.1 --- Cyclic-AMP (cAMP) level in rhTNF-treated L-929 cells --- p.102 / Chapter 5.2.2 --- Effect of intracellular cAMP level on rhTNF-mediated cytotoxicity on L-929 cells --- p.104 / Chapter 5.2.3 --- Effect of agonist and inhibitor of cAMP dependent protein kinase (protein kinase A) on rhTNF-mediated cytotoxicity on L-929 cells --- p.107 / Chapter 5.2.4 --- Effect of protein kinase A inhibitors on rhTNF-mediated cytotoxicity on L-929 cells --- p.111 / Chapter 5.3 --- Discussion --- p.118 / Chapter Chapter 6. --- "Role of intracellular free calcium, ions and calcium dependent response in rhTNF-mediated cytotoxicity on L-929 cells" --- p.121 / Chapter 6.1 --- Introduction --- p.121 / Chapter 6.1.1 --- Inositol triphosphate and intracellular free calcium --- p.121 / Chapter 6.1.2 --- Diacylglycerol --- p.131 / Chapter 6.1.3 --- Protein kinase C (PKC) --- p.131 / Chapter 6.1.4 --- Intracellular free calcium ions and protein kinase C --- p.134 / Chapter 6.1.5 --- Effect of intracellular free calcium ions and protein kinase C on TNF-mediated cytotoxicity --- p.135 / Chapter 6.1.6 --- Tyrosine kinase induced release of IP3 --- p.136 / Chapter 6.1.7 --- Calcium channels --- p.136 / Chapter 6.2 --- Result --- p.139 / Chapter 6.2.1 --- Effect of rhTNF on intracellular free [Ca2+] of L-929 cells --- p.141 / Chapter 6.2.2 --- Effect of calcium ion channel blockers on rhTNF-mediated cytotoxicity on L-929 cells --- p.148 / Chapter 6.2.3 --- Effect of protein kinase C (PKC) on rhTNF-mediated cytotoxicity on L-929 cells --- p.158 / Chapter 6.2.4 --- Immunofluorescence staining of PKC in rhTNF-treated L-929 cells --- p.162 / Chapter 6.2.5 --- Effect of calmodulin and calmodulin sensitive calcium ATPase on rhTNF-mediated cytotoxicity on L-929 cells --- p.165 / Chapter 6.2.6 --- Role of inositol triphosphate in rhTNF-mediated cytotoxicity on L-929 cells --- p.167 / Chapter 6.2.7 --- Role of tyrosine kinase activity in the rhTNF-mediated cytotoxicity on L-929 cells --- p.185 / Chapter 6.3 --- Discussion --- p.191 / Chapter Chapter 7. --- Effect of antioxidants on rhTNF-mediated cytotoxicity on L-929 cells --- p.195 / Chapter 7.1 --- Introduction: Oxygen free radicals as mediators of rhTNF-induced tumor cell necrosis --- p.195 / Chapter 7.2 --- Results --- p.199 / Chapter 7.3 --- Discussion --- p.203 / Chapter Chapter 8. --- General Discussion --- p.205 / Bibliography --- p.217

Ribonucleoproteins (RNPs) are RNA-protein complexes that carry out a variety of key cellular functions and are essential for the regulation of gene expression. Small nuclear RNPs (snRNPs) are a class of RNPs that regulate gene expression at the level of RNA processing in the nucleus. These RNPs are subject to complex and highly regulated biogenesis pathways in order to ensure sufficient snRNP levels are present within the cell. snRNPs are required for viability of all eukaryotic cells and the importance of proper snRNP function in vivo is further highlighted by the fact that the fatal motor neuron disease spinal muscular atrophy (SMA) is caused by a genetic deficiency in the ubiquitously expressed survival motor neuron (SMN) protein, an essential component of the snRNP biogenesis machinery. The most well characterized targets of SMN for RNP assembly are the spliceosomal snRNPs, which are critical factors that carry out pre-mRNA splicing. However, SMN is not believed to be solely dedicated to spliceosomal snRNP biogenesis but rather is thought to be a general RNP assembly machine. Yet, no other RNP targets of the SMN complex had previously been characterized in a conclusive manner. Understanding the cellular targets of SMN-mediated RNP assembly is critical for elucidating basic mechanisms of RNA regulation. Furthermore, despite increased understanding of the molecular function of SMN in spliceosomal snRNP biogenesis and the cellular basis of SMA in animal models, the molecular mechanisms through which loss of SMN function leads to motor neuron disease remain poorly defined. Thus, identifying additional RNP pathways that are dependent on SMN is key to uncover the molecular mechanisms of SMA and may also help in the design of novel therapeutic approaches to this devastating childhood disorder that is currently untreatable. In an effort to expand on the established RNP targets of SMN for assembly, in this dissertation I explore the hypothesis that SMN is required for the biogenesis and function of U7 snRNP and that disruption of this pathway induced by SMN deficiency contributes to motor neuron pathology in SMA. While structurally analogous to spliceosomal snRNPs, U7 snRNP functions not in splicing but rather in the unique 3’-end processing mechanism of replication-dependent histone mRNAs. Here, I first provide detailed molecular characterization of the in vivo functional requirement of SMN for U7 snRNP biogenesis as well as histone mRNA 3’-end processing and proper histone gene expression. I go on to demonstrate that in a mouse model of SMA U7 snRNP biogenesis and function are severely impaired by SMN deficiency and these defects occur in disease-relevant SMA motor neurons. I then describe the development of a novel molecular strategy to restore U7 snRNP activity in a setting of SMN deficiency in order to investigate the functional consequences of U7 dysfunction in SMA. Finally, I apply this U7 restoration strategy to a mouse model of SMA using AAV9-mediated gene delivery and establish that disrupted U7 activity contributes to select aspects of motor neuron dysfunction in SMA mice. Collectively, my dissertation work provides a significant expansion in our understanding of RNP pathways controlled by SMN and, for the first time, establishes the contribution of an SMN-dependent RNA pathway to SMA pathology in a mouse model of the disease that best recapitulates the human condition both genetically and phenotypically. The continuation of this work in the future not only may lead to a detailed molecular understanding of the mechanisms of SMA but possibly also to the development of novel therapeutic approaches for this deadly disease that are complementary to SMN upregulation.

In the eukaryotic nucleus, an immense length of DNA is compactly packaged to generate an ordered three-dimensional hierarchical structure called chromatin (van Holde, 1988; Wolffe, A.P, 1998). This organization forms a template for various DNA transaction processes like replication, transcription, recombination etc. The different stages of organization of the chromatin finally results in the 10,000-fold compaction observed in the metaphase chromosome. The problem of how the fibres of chromatin are folded has interested biologists and biochemists for decades. It has long been recognized that the Histones play a major part in this folding. However, the distinctly different roles of the Histones H2A, H2B, H3 and H4 on one hand and the lysine rich Histones such as Histone H1 and its cognates on the other, were not understood until after the discovery of the nucleosomes in the early 1970s. Some of the early insights into the structure of chromatin came through the digestion of nuclear chromatin with calcium-dependent endonucleases like micrococcal nuclease. A repeating kinetic intermediate of about 200 bp of DNA with Histones was obtained (Simpson, 1978). Based on repeating pattern of micrococcal nuclease digested chromatin and structural studies, Kornberg (1974) proposed that chromatin is composed of a flexible chain of repeating units of 100 A0 diameter. These units were termed as "nucleosomes" (Oudet et al, 1975). It then became clear that the Histones H2A, H2B, H3 and H4 were constituents of the nucleosome core particle whereas the lysine rich Histone H1 was somehow associated with the linker DNA between core particles. Hence, the formers are called core Histones and the latter as linker Histones. On further digestion of nucleosome, a nucleosome core was obtained in which wrapping of 146 bp of DNA about the Histone octamer to form the core particle provided the first level of folding. Electron microscopy and X-ray diffraction techniques suggested that this particle is a disk, 57 A0 thick and 110 A0 in diameter, and that the DNA is wound around the Histone core (Finch et al, 1977), But this cannot account for the many thousand-fold condensation of the DNA in the eukaryotic nucleus. The "string of beads" structure observed obviously could not satisfy the compaction requirement. It soon became evident that there exists some level of higher order folding of the chromatin fiber. In a classical paper, Finch and Klug (1976), showed that the extended nucleosomal filaments condense into irregular fibers of about 30 nm diameter in the presence of low concentrations of Mg 2+. Based on the data from earlier structural studies, these authors proposed a solenoid model in which nucleosomes were wrapped into a regular helix with a pitch of about 11nm. Later, it was observed that the formation of well defined fibers requires the presence of lysine rich Histones such as Histone H1.

Ribosome biogenesis is a crucial yet poorly understood and complex process in all cells. To date, most studies on eukaryotic ribosome biogenesis have relied on yeast genetics and whole cell analysis of ribosomal RNA processing. An early and critical step in ribosome biogenesis is the post-transcriptional modification of rRNA. Pseudouridylation is the most frequently occurring modification. Pseudouridylation is catalyzed by H/ACA small nucleolar ribonucleoproteins (snoRNPs) which are one of the two major classes of snoRNPs found within eukaryotes and archaea. H/ACA snoRNPs consist of four conserved core proteins Cbf5, Gar1, Nop10, and Nhp2 (eukaryotes), and a substrate specific H/ACA snoRNA. Mutations causing the rare inherited disease Dyskeratosis congenita are found in CBF5, NOP10, and NHP2. Here I report the purification of H/ACA protein Cbf5 in the presence of detergents. Additionally, I report initial in vitro RNA binding studies using Nhp2 and the snoRNA snR34 as well as the effects of Dyskeratosis congenita substitutions within Nhp2 on this interaction. / vii, 83 leaves : ill. ; 29 cm