Oxidative stress is considered a major factor in the etiology of age related diseases and the aging process itself. Organisms have developed mechanisms to protect against oxidative damage resulting from increased production of reactive oxygen species during aging. One of the major antioxidant systems is the methionine sulfoxide reductase (Msr) enzyme family. The two major Msr enzymes, MsrA and MsrB, can stereospecifically reduce the S and R epimers, respectively, of methionine sulfoxide in proteins back to methionine. This study, using Drosophila melanogaster, decribes the first animal system lacking both MsrA and MsrB. The loss of either MsrA or MsrB had no effect on lifespan in Drosophila, but loss of MsrB results in a slight decrease in locomotor activity from middle age onward. Double mutants lacking both forms of Msr have a significantly decreased lifespan and decreased locomotor activity at all ages examined. The double Msr mutants had no detectable increase in protein oxidation or decrease in mitochondrial function and were not more sensitive to oxidative stress. These results suggested that other cellular antioxidant systems were protecting the flies against oxidative damage and the decreased life span observed in the double knockouts was not due to widespread oxidative damage. However, one cannot exclude limited oxidative damage to a specific locus or cell type. In this regard, it was observed that older animals, lacking both MsrA and MsrB, have significantly reduced levels of dopamine, suggesting there might be oxidative damage to the dopaminergic neurons. Preliminary results also suggest that the ratio of F to G actin is skewed towards G actin in all mutants. The present results could have relevance to the loss of dopaminergic neurons in Parkinson’s disease. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2015 / FAU Electronic Theses and Dissertations Collection

Harman's theory of aging proposes that a buildup of damaging reactive oxygen species (ROS) is one of the primary causes of the deleterious symptoms attributed to aging. Cellular defenses in the form of antioxidants have evolved to combat ROS and reverse damage; one such group is the methionine sulfoxide reductases (Msr), which function to reduce oxidized methionine. MsrA reduces the S enantiomer of methionine sulfoxide, Met-S-(o), while MsrB reduces the R enantiomer, Met-R-(o). The focus of this study was to investigate how the absence of one or both forms of Msr affects locomotion in Drosophila using both traditional genetic mutants and more recently developed RNA interference (RNAi) strains. Results indicate that lack of MsrA does not affect locomotion. However, lack of MsrB drastically reduces rates of locomotion in all age classes. Furthermore, creation of an RNAi line capable of knocking down both MsrA and MsrB in progeny was completed. / by Kori Mulholland. / Thesis (M.S.)--Florida Atlantic University, 2013. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

Aging is a multifactoral biological process of progressive and deleterious changes partially attributed to a build up of oxidatively damaged biomolecules resulting from attacks by free radicals. Methionine sulfoxide reductases (Msrs) are enzymes that repair oxidized methionine (Met) residues found in proteins. Oxidized Met produces two enantiomers, Met-S-(o) and Met-R-(o), reduced by MsrA and MsrB respectively. Unlike other model organisms, our MsrA null fly mutant did not display increased sensitivity to oxidative stress or shortened lifespan, suggesting that in Drosophila, having either a functional copy of either Msr is sufficient. Here, two Msr mutant types were phenotypically assayed against isogenic controls. Results suggest that only the loss of both MsrA and MsrB produces increased sensitivity to oxidative stress and shortened lifespan, while locomotor defects became more severe with the full Msr knockout fly. / by Kelli Robbins. / Thesis (M.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

Chan Ka Ping Sophie. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 140-144). / Abstracts in English and Chinese. / Thesis/Assessment Committee --- p.i / Acknowledgements --- p.ii / Abstract --- p.viii / 摘要 --- p.x / Abbreviations --- p.xi / List of Figures --- p.xii / List of Tables --- p.xiv / Chapter 1 --- Introduction / Chapter 1.1 --- Pathogenesis of HBV Infection --- p.1 / Chapter 1.2 --- Classification and Structure --- p.2 / Chapter 1.3 --- HBV Genome --- p.4 / Chapter 1.4 --- Replication Cycle --- p.7 / Chapter 1.5 --- HBV Genotypes and Nomenclature --- p.9 / Chapter 1.5.1 --- Asian prevalent genotypes --- p.9 / Chapter 1.5.2 --- Numbering system --- p.9 / Chapter 1.6 --- Identification of Markers in HBV Genome for HCC Development --- p.11 / Chapter 1.7 --- Project Objective --- p.13 / Chapter 1.8 --- Promoters of HBV --- p.14 / Chapter 1.8.1 --- Pre-S1 promoter --- p.14 / Chapter 1.8.2 --- X promoter and enhancer I --- p.14 / Chapter 1.8.3 --- Core promoter and enhancer II --- p.15 / Chapter 1.8.4 --- Pair of mutations at BCP --- p.17 / Chapter 2 --- Materials and Methods / Chapter 2.1 --- Construction of pGL3-promoter Plasmids --- p.18 / Chapter 2.1.1 --- Templates selection --- p.18 / Chapter 2.1.2 --- Amplification of promoters --- p.19 / Chapter 2.1.3 --- Cloning into pGL3-basic vector --- p.21 / Chapter 2.1.4 --- Screening and plasmid preparation --- p.21 / Chapter 2.2 --- Construction of Mutant Promoter Clones --- p.23 / Chapter 2.2.1 --- Site-directed mutagenesis --- p.23 / Chapter 2.2.2 --- pPreS 1 /2712C mutant clone --- p.24 / Chapter 2.3 --- Cloning of Full-length HBV Genomes --- p.26 / Chapter 2.3.1 --- Replication-competent HBV clone --- p.26 / Chapter 2.3.2 --- Amplification of full-length HBV genome --- p.28 / Chapter 2.3.3 --- Cloning into pUC19 vector --- p.28 / Chapter 2.3.4 --- Screening for insert and sequence confirmation --- p.29 / Chapter 2.3.5 --- Excision of full-length HBV from plasmid --- p.29 / Chapter 2.4 --- Re-construction into a 1.3-fold HBV Clone --- p.32 / Chapter 2.4.1 --- Cloning of HBV fragment nucleotide 979-2617 (nt 979-2617) --- p.32 / Chapter 2.4.2 --- Screening for insert and sequence confirmation --- p.33 / Chapter 2.4.3 --- Cloning of HBV fragment (nt 905-2000) --- p.33 / Chapter 2.4.4 --- Construction of a 1.3-fold HBV genotype Cs clone --- p.34 / Chapter 2.5 --- Cell Culture --- p.37 / Chapter 2.5.1 --- Cell culture maintenance --- p.37 / Chapter 2.5.2 --- Transient transfection of promoter clones --- p.37 / Chapter 2.5.3 --- Transient transfection of HBV genomes --- p.38 / Chapter 2.6 --- Dual-Luciferase® Reporter Assay System --- p.40 / Chapter 2.6.1 --- Principle of the assay --- p.40 / Chapter 2.6.2 --- Cell harvest --- p.43 / Chapter 2.6.3 --- Luciferase assay --- p.43 / Chapter 2.7 --- Data Analysis --- p.44 / Chapter 2.8 --- Extraction of HBV DNA from Intracellular Cores --- p.45 / Chapter 2.8.1 --- Harvest of intracellular cores --- p.45 / Chapter 2.8.2 --- Phenol/chloroform extraction --- p.45 / Chapter 2.9 --- Southern Blotting --- p.47 / Chapter 2.9.1 --- Transfer of DNA to membrane --- p.47 / Chapter 2.9.2 --- Preparation of probes --- p.47 / Chapter 2.9.3 --- Hybridization with radiolabeled probes --- p.48 / Chapter 2.10 --- Detection of HBeAg and HBsAg --- p.50 / Chapter 2.10.1 --- HBsAg assays --- p.50 / Chapter 2.10.2 --- HBeAg assays --- p.51 / Chapter 2.11 --- SEAP Reporter Gene Assay --- p.52 / Chapter 3 --- Results / Chapter 3.1 --- Templates Selected --- p.53 / Chapter 3.2 --- Results of Luciferase Assays --- p.58 / Chapter 3.2.1. --- BCP mutation of genotype A as control --- p.58 / Chapter 3.2.2. --- Effect of C1165T mutation on Xpro/enhI activity of HBV genotype B --- p.60 / Chapter 3.2.3. --- Effect ofT2712C mutation on pre-S1 promoter activity of HBV Genotype B --- p.60 / Chapter 3.2.4. --- Effect of G1613A mutation on core pro/enhII activity of HBV Genotype Cs --- p.64 / Chapter 3.2.5. --- G1613A and BCP mutation --- p.67 / Chapter 3.3 --- Full-length HBV Genome Clones --- p.70 / Chapter 3.3.1. --- Construction of replication-competent full-length HBV genome clones --- p.70 / Chapter 3.3.2. --- Drawbacks of the system --- p.78 / Chapter 3.4 --- Construction of a Replication-competent 1.3-fold HBV Clone --- p.82 / Chapter 3.4.1. --- Construction of the HBV (nt 979-2617) clone --- p.82 / Chapter 3.4.2. --- Construction of the HBV (nt 905-2000) clone --- p.86 / Chapter 3.4.3. --- Construction of 1.3-fold genotype Cs HB V clone --- p.89 / Chapter 3.4.4. --- Test for replication competency --- p.92 / Chapter 4 --- Discussion / Chapter 4.1 --- BCP Mutation as Control of the Luciferase Assay --- p.94 / Chapter 4.2 --- Promoter Activities Not Altered by T2712C and C1165T --- p.96 / Chapter 4.3 --- Mutation G1613A of Core pro/enhll --- p.98 / Chapter 4.3.1 --- Mutation resides in negative regulatory element of core promoter --- p.98 / Chapter 4.3.2 --- NRE and NRE-binding protein --- p.98 / Chapter 4.3.3 --- Relationship with BCP mutation --- p.101 / Chapter 4.4 --- HBV Constructs --- p.103 / Chapter 4.4.1 --- Rationale in re-construction of 1.3-fold HB V clone --- p.103 / Chapter 4.4.2 --- Replication competency --- p.104 / Chapter 4.5 --- Conclusion --- p.106 / Chapter 4.6 --- Future Work --- p.107 / Appendix --- p.108 / References --- p.140

Fu Zhenming. / Thesis submitted in: December 2003. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 138-162). / Abstracts in English and Chinese. / List of abbreviations --- p.i / Abstract (in English) --- p.ii / 摘要（中文） --- p.iii / Acknowledgement --- p.iv / Chapter Chapter 1. --- Introduction and Objectives of Study --- p.1 / Chapter 1.1 --- Hepatocellular carcinoma in general --- p.2 / Chapter 1.1.1 --- "Epidemiology, risk factors" --- p.2 / Chapter 1.1.2 --- Pathology and staging --- p.4 / Chapter 1.1.3 --- Treatment --- p.6 / Chapter 1.1.4 --- Improvement of early detection and treatment of HCC --- p.7 / Chapter 1.2 --- General aspects of mitochondria and mitochondrial DNA (mtDNA) --- p.10 / Chapter 1.2.1 --- Structure and dynamics of mitochondria --- p.10 / Chapter 1.2.1.1 --- General introduction of mitochondria --- p.10 / Chapter 1.2.1.2 --- Respiration chain of mitochondria --- p.11 / Chapter 1.2.2 --- The mitochondrial genome --- p.14 / Chapter 1.2.2.1 --- Strucure --- p.14 / Chapter 1.2.2.2 --- Genes for structure proteins --- p.16 / Chapter 1.2.2.3 --- Genes for translation --- p.17 / Chapter 1.2.2.4 --- Imported proteins and RNAs --- p.17 / Chapter 1.2.3 --- Mitochondrial DNA maintenance --- p.19 / Chapter 1.2.4 --- Mitochondrial DNA replication --- p.25 / Chapter 1.2.5 --- Mitochondrial DNA transcription --- p.30 / Chapter 1.2.6 --- Mitochondrial DNA translation --- p.32 / Chapter 1.3 --- MtDNA diseases --- p.35 / Chapter 1.4 --- MtDNA mutation and HCC --- p.35 / Chapter 1.5 --- Aims of the study --- p.39 / Chapter Chapter 2. --- Materials and Methods --- p.41 / Chapter 2.1 --- Materials --- p.42 / Chapter 2.1.1 --- Chemicals --- p.42 / Chapter 2.1.2 --- Primers --- p.42 / Chapter 2.1.3 --- Enzymes --- p.45 / Chapter 2.1.4 --- Cell line --- p.45 / Chapter 2.1.5 --- Collection of specimens --- p.46 / Chapter 2.2 --- Methodology --- p.47 / Chapter 2.2.1 --- "DNA extraction from hcc tissues, cell line Hep3B and PBMCs" --- p.47 / Chapter 2.2.1.1 --- DNA extraction from HCC tissues --- p.47 / Chapter 2.2.1.2 --- DNA extraction from cell line Hep3B --- p.49 / Chapter 2.2.1.3 --- DNA extraction from and PBMCs --- p.50 / Chapter 2.2.1.3.1 --- Preparation of PBMCs --- p.50 / Chapter 2.2.1.3.2 --- DNA extraction from and PBMCs --- p.51 / Chapter 2.2.2 --- Detection of mt whole genome mutation by direct sequencing --- p.51 / Chapter 2.2.2.1 --- Design of mtDNA primers --- p.51 / Chapter 2.2.2.2 --- PCR amplification of the whole mt genome --- p.51 / Chapter 2.2.2.3 --- Direct sequencing of the whole mt genome --- p.52 / Chapter 2.2.2.3.1 --- Primer used in sequencing --- p.52 / Chapter 2.2.2.3.2 --- Purification of the PCR products of the whole mt genome --- p.53 / Chapter 2.2.2.3.3 --- Dye terminator cycle sequencing reaction --- p.53 / Chapter 2.2.2.3.4 --- Purification of extension products --- p.54 / Chapter 2.2.3 --- Detection of mtDNA control region mutation --- p.55 / Chapter 2.2.3.1 --- PCR amplification of D310 in the mtDNA control region --- p.55 / Chapter 2.2.3.2 --- Screening of D310 mutation by PFLDA --- p.55 / Chapter 2.2.3.2.1 --- Making 8% denatured gel mixture --- p.55 / Chapter 2.2.3.2.2 --- Setting up and Pouring the denatured gel --- p.56 / Chapter 2.2.3.2.4 --- Preparing and Loading the PCR products --- p.57 / Chapter 2.2.3.2.5 --- Electrophoresis --- p.57 / Chapter 2.2.3.2.6 --- "Gel fixing, silver staining and color development " --- p.58 / Chapter 2.2.3.3 --- Direct sequencing of D310 in the mtDNA control region --- p.59 / Chapter 2.2.4 --- Detection of mt DNA coding region mutation --- p.60 / Chapter 2.2.4.1 --- PCR amplification of the 5 respiratory chain subunit genes --- p.60 / Chapter 2.2.4.2 --- Restriction enzyme digestion of 5 genes in mtDNA coding region --- p.60 / Chapter 2.2.4.3 --- Screening of mtDNA coding region mutation by SSCP --- p.61 / Chapter 2.2.4.3.1 --- Making 6% 49:1 acrylamide/Bis SSCP gel mixture --- p.61 / Chapter 2.2.4.3.2 --- "Setting up the SSCP gel, loading sample, fixing, staining and developing of the gel " --- p.62 / Chapter 2.2.4.4 --- Sequencing conformation of the mtDNA coding region mutation --- p.62 / Chapter 2.2.5 --- Statistics --- p.63 / Chapter 2.2.5.1 --- The chi-square test --- p.63 / Chapter 2.2.5.2 --- The Friedman test --- p.63 / Chapter 2.2.5.3 --- Wilcoxon signed ranks test --- p.63 / Chapter Chapter 3. --- Results --- p.64 / Chapter 3.1 --- Detection mt DNA whole genome mutation --- p.65 / Chapter 3.1.1 --- Identification of mtDNA whole genome by direct sequencing --- p.65 / Chapter 3.2 --- Detection mt DNA D-loop mutation --- p.76 / Chapter 3.2.1 --- Screening of C-tract alteration in HCC tissus by PCR fragments length detection assay (PFLDA) --- p.76 / Chapter 3.2.2 --- Screening of coding region alteration in HCC tissues by SSCP --- p.77 / Chapter 3.2.2.1 --- Identification of C-tract alterations in HCC and non-tumorous tissues by direct sequencing --- p.77 / Chapter 3.2.3 --- Identification of C-tract alterations by direct sequencing --- p.82 / Chapter 3.2.3.1 --- Identification of C-tract alterations in HCC tissues by direct sequencing --- p.82 / Chapter 3.2.3.2 --- Identification of C-tract alteration in PBMC of normal subjects by direct sequencing --- p.82 / Chapter 3.2.3.3 --- Identification of C-tract alteration in PBMC of HCC patients by direct sequencing --- p.82 / Chapter 3.2.4 --- Statistics of the analysis of C-tract alterations --- p.82 / Chapter 3.3 --- Detection mt DNA mutation in the coding region --- p.87 / Chapter Chapter 4. --- Discussion --- p.98 / Chapter 4.1 --- Detection mtDNA whole genome mutation --- p.99 / Chapter 4.2 --- Detection mtDNA D-loop mutation --- p.107 / Chapter 4.3 --- Detection mtDNA mutation in the coding region --- p.119 / Chapter 4.4 --- Possible mechanisms of mtDNA mutation in HCC carcinogenesis --- p.125 / Chapter 4.5 --- Proposals for prospective studies --- p.126 / Chapter 4.5.1 --- Function of C7 in D310 --- p.128 / Chapter 4.5.2 --- Function changes of mtDNA coding region mutation --- p.130 / Chapter 4.5.3 --- Detection of D310 C-tract mutation in patients' plasma --- p.131 / Chapter 4.5.4 --- Relationship between nMSl and mtMSI --- p.132 / Chapter 4.6 --- Summary --- p.134 / References --- p.137

Orientadores: Maricilda Palandi de Mello, Celso Eduardo Benedetti, Fernanda Caroline Soardi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-15T21:27:39Z (GMT). No. of bitstreams: 1 CunhaJunior_JoseLuizRosenberis_M.pdf: 3002580 bytes, checksum: 1980aba7f72fdfd74e758a924771c055 (MD5) Previous issue date: 2010 / Resumo: A expressão do gene SRY (Sex Determining Region in chromosome Y) é responsável por desencadear a determinação testicular durante o desenvolvimento embrionário, a partir das gônadas ainda indiferenciadas. Mutações nesse gene são encontradas em muitos casos de anomalias do desenvolvimento gonadal. O projeto teve por objetivo principal a análise funcional do efeito de uma mutação na região promotora do gene SRY, sendo que essa mutação consiste em uma deleção de 3 pares de base em um dos sítios consenso de ligação do fator de transcrição Sp1 ao promotor do gene. O portador dessa mutação é um indivíduo com disgenesia gonadal pura 46,XY, sendo que outros membros da família apresentavam ambiguidade genital e o pai, também portador da mutação, possuía grave hipospadia ao nascimento. Para tentar esclarecer os efeitos desta mutação nos mecanismos moleculares de regulação da expressão do gene SRY, este trabalho primeiramente analisou a interação da proteína Sp1 com os sítios localizados na região promotora de SRY e o efeito da mutação nesta interação, através de ensaios de EMSA (Electrophoretic Mobility Shift Assay). Concluiu-se que os sítios Sp1A e Sp1B se ligam a duas moléculas de Sp1 e que a mutação no Sp1A praticamente abole esta ligação. Possivelmente a ausência dessa ligação impediu a formação de um complexo de transcrição, causando uma diminuição na expressão do gene SRY e levando à ausência de formação dos testículos e reversão sexual completa na paciente. Complementando, foi analisado o efeito dessa mutação na expressão através de ensaio de expressão com gene repórter, no qual o promotor normal se mostrou em média duas vezes mais eficiente na ativação da expressão da luciferase que o promotor mutante. Entretanto, mais experimentos de transfecção, inclusive com outras linhagens celulares, devem ser realizados para confirmação desse resultado. Além disso, foi analisado o efeito de uma nova mutação (localizada na região codificante do gene SRY) na ligação da proteína SRY com o DNA, através de ensaios de EMSA. Concluiu-se que a mutação E89K, associada com disgenesia gonadal pura 46,XY, reduziu em alto nível a atividade de ligação in vitro da proteína SRY mutante ao DNA, o que representa um forte indício de que atividade reduzida da proteína mutante não foi suficiente para desencadear o processo de determinação testicular. Paralelamente, foi feito o rastreamento de mutações no gene SRY e sua região promotora em novos casos de disgenesia gonadal, não tendo sido encontradas, porém, alterações nos pacientes analisados / Abstract: The SRY (Sex Determining Region in chromosome Y) gene expression is responsible for testicular determination during embrionary development. Mutations in SRY are found in many cases of anomalies of gonadal development. This project analyzed the functional effect of a mutation in SRY promoter region; the mutation is a 3-bp deletion in a consensus binding site for Sp1 transcription factor. The patient presented 46,XY pure gonadal dysgenesis, and a family history of relatives with different levels of genital ambiguity. Her father shares the same mutation in the SRY promoter region. In order to investigate the effects of the mutation upon the molecular mechanisms that regulate SRY gene expression, the interaction of the Sp1 transcription factor with normal and mutant binding sites was analyzed by EMSA (Electrophoretic Mobility Shift Assay). Each of Sp1A and Sp1B normal sites binds to a single Sp1 molecule, whereas the 3-bp deletion in Sp1A abolishs the binding to this site. Probably, the lack of Sp1 binding to the Sp1A site prevented the formation of a stable transcription complex, reducing the level of SRY expression and leading to the absence of testicles and complete sex reversal in the patient. Parallely, the effect of the mutation was analyzed by a reporter gene assay, indicating that the normal promoter is almost two times more efficient than the mutant promoter in the activation of luciferase gene expression using HeLa cells. However, further transfection experiments with other cell lineages must be performed to confirm this result. In addition, the effect of a new mutation (E89K, located in the SRY gene coding region) was analyzed by testing the ability of the SRY mutant protein to bind its DNA consensus sequence. EMSA assays revealed that the E89K mutation, which is associated with 46,XY pure gonadal dysgenesis, strongtly reduced the SRY protein binding activity in vitro. This result is a strong evidence that the reduced activity of SRY mutant protein was not sufficient to trigger the testicular determination in the patient, leading to the pure gonadal dysgenesis phenotype. Screening of mutations in the SRY gene coding and promoter regions was also performed in six diferent patients with 46,XY gonadal dysgenesis. However, other mutations have not been identified / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Orientadores: Hyun Mo Yang, Norberto Anibal Maidana / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação Científica / Made available in DSpace on 2018-08-20T00:06:51Z (GMT). No. of bitstreams: 1 Malaquias_AngeloMiguel_D.pdf: 3743949 bytes, checksum: d321f27ce84d0589990109a3ee8d2ab3 (MD5) Previous issue date: 2012 / Resumo: Esta tese tem como objetivo abordar, matematicamente, a mutação do vírus da imunodeficiência humana (HIV) por meio de um processo de difusão e advecção. é dividida em três partes: estudo e compreensão do fenômeno biológico; formulação e análise de um primeiro sistema de equações diferenciais ordinárias para estudar o tema e, finalmente, construção e análise de um modelo de equações diferenciais parciais envolvendo a mutação. Os modelos são formulados com base em características biológicas, e procurando, sempre que possível, estabelecer um paralelo entre Biologia e Matemática. Com o modelo de equações diferenciais ordinárias mostrou-se que um sistema imunológico que perde sua capacidade de resposta permite a persistência do vírus HIV no organismo infectado. Também, do modelo com equações diferenciais parciais, concluímos que usar as próprias mutações para combater o vírus pode ser uma alternativa, assim como na idéia de mutagênese letal / Abstract: The aim of this thesis is to study mathematically the mutation of the human immunodeficiency virus (HIV) taking into account the process of diffusion and advection. The thesis is divided in three parts: the current understand of the HIV biology; formulation and analysis of a system of ordinary differential equations to understanding the persistent HIV infection; and, finally, construction and analysis of a model of partial differential equations considering the mutation. The models are formulated based on biological characteristics and whenever it is possible, a parallel between biology and mathematics was established. From system of ordinary differential equations, the persistent HIV infection can be explained by exhausting immune system response. From partial differential equations, the main conclusion is that mutations themselves can be used to fight the virus based on the idea of lethal mutagenesis / Doutorado / Matematica Aplicada / Doutor em Matemática Aplicada

Submitted in the fulfillment of the requirement for the Degree of Master's in Chemistry, Durban University of Technology, 2017. / P53 is a tumour suppressor protein that is dysfunctional in most human cancer cells. Mutations in the p53 genes result in the expression of mutant proteins which accumulate to high levels in tumour cells. Several studies have shown that majority of the mutations are concentrated in the DNA-binding domain where they destabilize its conformation and eliminate the sequence- specific DNA-binding to abolish p53 transcription activities. Accordingly, this study involved an investigation of the effects of mutations associated with cancer, based on the framework of sequences and structures of p53 DNA-binding domains, analysed by SIFT, Pmut, I-mutant, MuStab, CUPSAT, EASY-MM and SDM servers. These analyses suggest that 156 mutations may be associated with cancer, and may result in protein malfunction, including the experimentally validated mutations. Thereafter, 54 mutations were further classified as disease- causing mutations and probably have a significant impact on the stability of the structure. The detailed stability analyses revealed that Val143Asp, Ala159Pro, Val197Pro, Tyr234Pro, Cys238Pro, Gly262Pro and Cys275Pro mutations caused the highest destabilization of the structure thus leading to malfunctioning of the protein. Additionally, the structural and functional consequences of the resulting highly destabilizing mutations were explored further using molecular docking and molecular dynamics simulations. Molecular docking results revealed that the p53 DNA-binding domain loses its stability and abrogates the specific DNA-binding as shown by a decrease in binding affinity characterized by the ZRANK scores. This result was confirmed by the residues Val143Asp, Ala159Pro, Val197Pro, Tyr234Pro and Cys238Pro p53-DNA mutant complexes inducing the loss of important hydrogen bonds, and introduced non-native hydrogen bonds between the two biomolecules. Furthermore, Molecular dynamics (MD) simulations of the experimental mutant forms showed that the structures of the p53 DNA-binding domains were more rigid comparing to the wild-type structure. The MD trajectories of Val134Ala, Arg213Gly and Gly245Ser DNA-binding domain mutants clearly revealed a loss of the flexibility and stability by the structures. This might affect the structural conformation and interfere with the interaction to DNA. Understanding the effects of mutations associated with cancer at a molecular level will be helpful in designing new therapeutics for cancer diseases. / M

Orientadores: Maricilda Palandi de Mello, Monica Barbosa de Melo, Fernanda Caroline Soardi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T10:51:43Z (GMT). No. of bitstreams: 1 Franca_EmersonSalvadordeSouza_M.pdf: 3804995 bytes, checksum: 694d80ade56340a0a1125338c03238ad (MD5) Previous issue date: 2009 / Resumo: O gene PAX6 é o principal gene para o controle da organização do sistema ocular durante a embriogênese. Este gene pertence a uma família de reguladores de transcrição denominada PAX, sendo que seus membros compartilham um domínio funcional de 128 aminoácidos chamado de paired domain. O PAX6 é o mais bem estudado dessa família. O gene PAX6 está localizado na banda 13 do braço curto do cormossomo11 em humanos, e apresenta 14 exons sendo que os três primeiros e parte do quarto exon não são traduzidos. A proteína do PAX6 possui dois domínios funcionais: o paired domain e o homeo domain, que são separados por um segmento de ligação denominado LNK e seguidos por uma região com importante função na ativação transcricional denominada PST. A proteína do gene PAX6 é um fator de regulação transcricional altamente conservado com funções importantes para o desenvolvimento normal dos olhos e do sistema nervoso. Alterações no gene PAX6 em humanos foram associadas ao fenótipo de aniridia, da síndrome de Morning Glory (MGS) e também de doenças associadas ao desenvolvimento ocular. A aniridia é um defeito congênito raro, a qual provoca uma formação incompleta ou a ausência da íris. Embora seus efeitos variem entre os indivíduos, pode causar perda de visão. A doença pode ser de herança autossômica dominante ou de manifestação esporádica. MGS é uma anomalia congênita do nervo óptico, comumente unilateral, podendo encontrar-se associada estrabismo, ambliopia e nistagmo. Freqüentemente essa síndrome pode encontrar-se associada a anomalias endócrinas, renais e do sistema nervoso central. Sendo assim, o projeto teve por objetivos a análise molecular do gene PAX6 através de seqüenciamento e da técnica de MLPA em pacientes com aniridia e pacientes portadores da síndrome de MGS, a fim de se detectar mutações e/ou polimorfismos que pudessem estar ligados ao quadro clínico dos indivíduos. A casuística do projeto foi de três famílias com segregação aniridia, um indivíduo esporádico com aniridia e quatro indivíduos portadores da síndrome de Morning Glory. O grupo controle consistiu de 50 indivíduos triados como não tendo alterações oftalmológicas. Foi encontrada uma mutação p.R240X no gene PAX6, que causa uma troca de uma arginina por um stop codon, segregando nos indivíduos afetados da Família 1 e assim explicando o fenótipo dos indivíduos. Essa mutação é a mais freqüente associada à aniridia, porém é a primeira vez que ela foi descrita na população brasileira. Também foram encontradas diversas alterações descritas e não descritas que necessitam de mais estudos para que possam ser associadas à manifestação do fenótipo dos indivíduos afetados. Além disso, foi observada pela técnica de MLPA, uma possível micro-deleção ou alteração nucleotídica no exon 1 do gene RCN1 encontrada nos filhos das Famílias 1 e 3 podendo estar envolvida na regulação 5' do gene PAX6. Outra possível micro-deleção ou alteração nucleotídica foi também observada no exon 9 do gene ELP4, que pode estar associada a regulação 3' do gene PAX6. Esse estudo demonstrou que para a etiologia de aniridia e síndrome Morning Glory devem existir outros genes cuja expressão possa estar alterada durante o desenvolvimento. / Abstract: PAX6 gene is the major gene in the control of eye organization during development. It belongs to a family of transcription regulators called PAX, formed by several members which share a 128 aminoacid functional domain called paired domain. PAX6 is best studied within this family. In humans, it is located on chromosome 11p13 and is formed by 14 exons; the first three and part of the fourth are not translated. PAX6 protein comprises two functional domains: the paired domain and the homeo domain which are separated by a linker called LNK and followed by an important region with trancriptional activity called PST. The PAX6 protein is a highly conserved transcriptional regulator factor that is important for normal ocular and neural development. Mutations on human PAX6 gene were associated to aniridia, Morning Glory Syndrome and other ocular diseases. Aniridia is rare birth defect which leads to an incomplete formation or the absence of the iris. Although their effects vary between individual, aniridia can cause loss of vision. The disease may be autosomal dominant or sporadic event. The Morning Glory Syndrome (MGS) is a congenital optic disk dysplasia, generally unilateral, which can be associated with strabismus, amblyopia and nystagmus. This syndrome may be often associated with endocrine, renal and central nervous system abnormalities. Thus the aim of this investigation was to evaluate the molecular composition of PAX6 gene using direct sequencing and MLPA technique in patients with Aniridia and Morning Glory Syndrome, to detect mutations and/or polymorphisms associated with the patient's phenotypes. Were included in the study 1 family with segregation of aniridia, 1 family with Axenfeld-Rieger Syndrome, 1 sporadic individual with aniridia and 4 individuals carrying MGS. The control group comprised 50 individuals considered ophthalmologically normal. The nonsense mutation p.R240X was found in the PAX6 gene, segregating with the affected members in family 1, what explains their phenotypes. This mutation is one of the most frequent nonsense mutations associated with the aniridia, however this is the first report on a PAX6 gene mutation familial case of aniridia in Brazil. Several described and non-described nucleotide variations were found, but additional studies are required to correlate them to the phenotype of affected individuals. Furthermore, the MLPA technique showed possible micro-deletions or mutations in exon 1 of RCN1 gene, located 5' to PAX6. This result was observed in both male children of families 1 and 3. Other possible micro-deletion or mutation was observed in exon 9 of ELP4 gene, which can be associated to 3' regulation of PAX6 gene. This study demonstrated that the involvement of other gene whose expressions may be altered during the development cannot be excluded for the etiology of aniridia and Morning Glory Syndrome. / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009.