Genetic factors play an important role in the pathogenesis of Paget’s Disease of Bone (PDB). The most important predisposing gene is SQSTM1 which is mutated in about 10% of patients, additionally common variants at seven other loci have also been shown to predispose to PDB as well as environmental factors which are also important in the pathogenesis of PDB. Little research has been conducted on the relationship between the genetic variants that predispose to PDB and disease severity. Similarly, only limited information exists on the role that gene-environment interactions play in the pathogenesis of PDB or its severity. The aim of the present thesis was to explore these issues in participants of the Paget’s Disease Randomised Trial of Intensive versus Symptomatic Management study (PRISM) and other study cohorts. In chapter 3, I investigate the relationship between SQSTM1 mutation status, disease severity and clinical outcome in 737 patients from the PRISM study. Mutations of SQSTM1 were detected in 80/737 (10.9%) patients. Mutation carriers had an earlier age at diagnosis; a greater number of affected bones and more commonly had required orthopaedic surgery and bisphosphonate therapy than those without mutations. Quality of life was significantly reduced in carriers and during the study; fractures were more common although most of these occurred in unaffected bone. This study demonstrates that SQSTM1 mutations are strongly associated with disease severity and complications of PDB. In chapter 4, I study associations between common genetic variants identified by genome wide association (GWAS), clinical severity and extent of PDB, alone and in combination with SQSTM1 mutations. This showed that these common variants were also associated with severity and extent of PDB in PRISM, but with weaker effects than SQSTM1 mutations. The findings were replicated in a multinational study involving 1940 subjects from centres in Italy, Spain and Australia. In all cohorts the GWAS risk alleles acted in an additive manner with SQSTM1 mutations to regulate disease severity and extent. By combining information from SQSTM1 status and the new risk alleles, however, we are able to develop a genetic risk score which delineated three distinct groups with markedly differing effects on disease extent and severity. In chapter 5, I study associations between PDB, severity and extent in relation to circulating levels of IgG antibodies against various viruses including Rubella, respiratory syncytial virus, distemper, varicella zoster virus, measles and mumps. We found little evidence of an interaction between viral antibody titres and SQSTM1 in predicting disease severity with the notable exception of mumps virus where subjects with the highest levels of antibodies that were SQSTM1 positive had in increased age at diagnosis than the other genotype / viral antibody groups. Overall the studies do provide no support for the notion that patients with PDB have an abnormal antibody response to paramyxovirus or have had previous infections with these viruses more frequently than controls. This of course does not exclude the possibility that PDB patients might have a clinically occult slow virus infection which is not accompanied by an abnormality in the immune response. . This raises the possibility that genetic testing may be of value in identifying individuals at risk of developing severe disease and those at risk of complications. I also demonstrate that PBD patients have abnormalities in circulating antibodies to various viruses suggesting that the disease may be associated with disturbance in the response of the immune system to infectious agents but further investigation is required. This, perhaps, could explain the changes in the severity and prevalence of PDB that have been observed over recent years in several countries.

Made available in DSpace on 2014-10-09T12:54:42Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:08:00Z (GMT). No. of bitstreams: 0 / Até pouco tempo, o conhecimento da contaminação dos ecossistemas aquáticos, estava restrito a metais e agrotóxicos, sendo pouca ênfase dada a produtos farmacêuticos, que, apesar de serem encontrados em concentrações de nanogramas a microgramas, podem causar efeitos letais e induzir malformações nos organismos. Estudos ecotoxicológicos têm sido realizados para identificar os efeitos destas substâncias, contudo, os dados são insuficientes, principalmente no que se refere a efeitos subletais e de toxicidade em espécies de ambientes tropicais e subtropicais. Efeitos letais e subletais, como crescimento e reprodução, são determinados através de ensaios ecotoxicológicos agudos e crônicos, sendo as malformações dificilmente evidenciadas por estes ensaios. Diante disto, pesquisadores vêm desenvolvendo metodologias mais refinadas, como por exemplo, a exposição direta de embriões a produtos químicos em ensaios de teratogênese. Para Cladocera estes ensaios são restritos. O objetivo deste trabalho foi estudar os efeitos letais e subletais de um antimicrobiano, Triclosan, através de ensaios de ecotoxicidade com Daphnia similis, Ceriodaphnia. dubia e C. silvestrii. A fim de se estimar com maior rigor os efeitos em ambientes tropicais e subtropicais, os ensaios foram realizados com água natural como água de diluição, com e sem fotoperíodo. Também foram realizados ensaios em água Milli- Q água reconstituída, sem fotoperíodo de modo a observar a toxicidade do produto sem interferentes externos. Estágio do desenvolvimento embrionário de D. similis, C. dubia e C. silvestrii foram identificado de modo a otimizar os ensaios de teratogênese. Para o estudo da toxicidade, foram realizados ensaios de ecotoxicidade aguda com D. similis, C. dubia e C. silvestrii e ensaios crônicos com D.similis e C. silvestrii. Para a classificação dos estágios do desenvolvimento embrionário, ovos foram cultivados in vivo a temperatura de 20°C (D. similis) e 25°C (C. dubia e silvestrii), observados a cada hora, até o desenvolvimento completo do organismo. Posteriormente, as condições dos ensaios de teratogênese foram estabelecidas sendo realizados com D. similis. A CE50 48H de Triclosan para D.similis e C. silvestrii em água natural reconstituída com fotoperíodo foi de 0,23 e 0,10 mg.L-1, respectivamente, e de 0,13 mg.L-1para C. silvestrii, sem fotoperíodo. Para os ensaios com água Milli-Q reconstituída, sem fotoperíodo, os valores de CE50;48H para D. similis, C. dubia e C. silvestrii foram de 0, 22; 0,09 e 0,08 mg.L-1, respectivamente. O CEO para D. similis foi de 0,1 mg.L-1 e a o valor de IC50 relativo às malformações das neonatas nos testes crônicos foi de 0,057 mg.L-1. Para C.silvestrii o CEO foi de 0,04 mg.L-1, não sendo evidenciadas malformações nas neonatas. Sete estágios foram observados no desenvolvimento embrionário dos cladoceros com duração (horas) de 34 (±3) para C. dubia, 36(±2) para C. silvestrii e de 51 (±5) para D. similis. O valor de IC50 para malformação nos ensaios de teratogênese (exposição direta de embriões) para D. similis foi de 0,075 mg.L-1, próximo ao obtido nos ensaios crônicos / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energéticas e Nucleares - IPEN/CNEN-SP

Abstract In the present study, mutations in BRCA1 and BRCA2, the two major genes predisposing individuals to hereditary breast and ovarian cancer, were screened in Finnish and Turkish cancer families. Germline BRCA1 mutations were found in 7% (6/88) and BRCA2 mutations in 6% (5/88) of the Finnish families studied in Oulu. Two distinct BRCA1 (3745delT, 4216nt-2A→G) and three BRCA2 (999delTCAAA, 6503delTT, 9346nt-2A→G) mutations were identified, all of which are recurrently found in Finland. In the 15 Turkish cancer families studied, 5382insC and 5622C→T were detected in BRCA1, and 3414delTCAG in BRCA2. The novel 3414del4 mutation was found in a family with a case of male breast cancer. In order to determine their ages and origin, 9 recurrent Finnish BRCA1 and BRCA2 mutations were studied further as regards haplotype conservation. Common origins approximately 18–80 generations (400–1600 years) ago were demonstrated for all studied mutations by partial haplotype sharing. The majority of the mutations showed geographical clustering, supporting the theory of regional founder effects. Four of the nine mutations are unique for Finland, whereas five have also been seen elsewhere. Mutations in the 5' end of BRCA1 tend to predispose individuals to ovarian cancer and those found in the 3' end to breast cancer. The age of ovarian cancer onset was significantly lower for BRCA1 (51 years) than for BRCA2 mutation carriers (61 years). Germline TP53 mutations were sought in the Finnish breast cancer families found to be negative after BRCA1 and BRCA2 screening but who exhibited some phenotypic features of the Li-Fraumeni syndrome. The Asn235Ser was found in a family displaying Li-Fraumeni syndrome phenotype and the Tyr220Cys in a family with a milder Li-Fraumeni-like phenotype. The nature of both mutations as cancer-predisposing alterations was supported by means of loss of heterozygosity (LOH) and p53 immunohistochemistry studies. Regional clustering of BRCA1 and BRCA2 founder mutations enables targeted genetic tests including especially those mutations characteristic of the birthplace of each patient. Additional genes are likely to explain a large proportion of the inherited susceptibility to breast cancer in particular. Germline TP53 mutations are expected to be found in the breast cancer families with other clinical features seen in the Li-Fraumeni syndrome.

The role of individual amino acid residues of the enzyme dienelactone hydrolase was investigated. Using the polymerase chain reaction (PCR), a 1.9 kbp clcD fragment was amplified and subcloned yielding a 821 bp BamHI to EcoRI clcD subclone in the plasmid pUC19. Site-specific mutants of dienelactone hydrolase were created using mismatched oligonucleotides to prime DNA synthesis. Specifically modified proteins from mutated clcD genes (Arg 81 to alanine, Tyr 85 to phenylalanine and Arg 206 to alanine), were encoded by the mutant clones. Enzyme assays showed that dienelactone hydrolase activity of the mutants Arg 81 and Arg 206 was totally abolished. The DLHase enzyme activity of mutant Tyr 85 is greatly decreased by approximately two thirds.

RNA molecules interact by forming inter-molecular base pairs that compete with the intra-molecular base pairs of their secondary structures. Here we investigate the patterns of neutral mutations in RNAs whose function is the interaction with other RNAs, i.e., the co-folding with one or more other RNA molecules. We find that (1) the degree of neutrality is much smaller in interacting RNAs compared to RNAs that just have to coform to a single externally prescribed target structure, and (2) strengthening this contraint to the conservation of the co-folded structure with two or more partners essentially eliminates neutrality. It follows that RNAs whose function depends on the formation of a specific interaction complex with a target RNA molecule will evolve much more slowly than RNAs with a function depending only on their own structure.

MSc (Med), Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand / Factor X deficiency is a rare bleeding disorder with an incidence of one in a million in the general population. Patients with the severe form of factor X deficiency suffer from serious bleeds occurring mainly into the joints and the muscle. In the two factor X deficient families currently looked after at the Haemophilia Comprehensive Care Centre, there are definite differences in the bleeding tendencies between and within family members. We hypothesize the differences in genetic mutations and the influence of cytokines to be responsible for these bleeding variabilities. These factors were explored in our study. The study population included a total of fourteen members of the two families with factor X deficiency. Blood for factor X measurement, cytokine studies and genetic studies was collected in the Haemophilia Comprehensive Care Centre of the Charlotte Maxeke Johannesburg Academic Hospital. Each blood was processed according to the test to be performed. Factor X activity levels were measured using the factor X assay, and the information on each patient’s bleeding episodes was obtained from the Haemophiliac Clinic database. Cytokines were analyzed in all patients using the ELISA kits from Biosource. Factor X gene was amplified using PCR and sequenced with Spectrumedix SCE 2410. iv For cytokine studies, high levels of IL-1beta and TNF-alpha were observed in frequent bleeding patients compared to infrequent bleeders. These cytokines are known to be involved in acute inflammatory process leading to cellular infiltrate and joint swelling. This results in synovitis and the creation of massive joint bleeding. The low levels of IL-1beta and TNF-alpha detected in infrequent bleeding patients appear to be related to the high levels of IL-1Ra and IL-10. These anti-inflammatory cytokines are known to inhibit the inflammatory synovitis and lessen the severity of joint bleeding. For genetic studies, differences were observed between the amino acid sequence of the three frequent bleeding patients and the consensus. In addition, a novel mutation Cys350Phe was detected in two of these patients. This mutation is characterized by very low factor X levels which sometimes are not detectable in circulation. The substituted cystine is known to cause defect in the substrate binding, leading to the lost of enzyme activity. From these findings we have concluded that the origin of the heterogeneity of bleeding in factor X deficiency is multifactorial, cytokines and genetic mutations seems to have a role in determining the clinical manifestations of the factor X deficient patients.

ABCB11/BSEP est le transporteur des acides biliaires, localisé au niveau du pôle canaliculaire des hépatocytes. Les mutations de ce gène sont responsables de la cholestase familiale intrahépatique progressive de type 2.Au cours de ma thèse, j’ai évalué la capacité des aminoglycosides et du PTC124 à induire la translecture de codons stop prématurés, l’adressage et la fonction de mutants non-sens et faux sens de Bsep ainsi que l’effet d’une bithérapie (translecture+chaperone).Dans nos modèles cellulaires, la gentamicine était capable d’induire la translecture du codon-stop prématuré du mutant non-sens BsepR1090X dans les lignées NIH3T3, HEK293 et Can 10. La protéine entière générée était partiellement détectée aux membranes plasmiques des cellules HEK293 et canaliculaires des cellules Can 10 et était partiellement fonctionnelle puisqu’elle était responsable d’une augmentation de l’activité de transport de 3H-taurocholate (3H-TC) dans les clones MDCK. Ces effets étaient potentialisés par l’addition de drogues chaperones telles que le 4-phenylbutyrate (4-PB).J’ai également mis en évidence la capacité de nouveaux composés dérivés du 4-PB (MHMPB, OTNC et HMPB) à corriger l’adressage et à augmenter le transport de 3H-TC du mutant faux sens BsepR1128C à des concentrations plus faibles que le 4-PB. Enfin, j’ai pu montrer que d'autres drogues chaperones (GPB, PA, SAHA et C18), pouvaient corriger l’adressage canaliculaire de BsepR1128C et augmenter son activité de transport de 3H-TC dans les clones MDCK. / ABCB11/BSEP is the main bile acids transporter located at the canalicular pole of hepatocytes. Mutations of ABCB11 are responsible for progressive familial intrahepatic cholestasis type 2.During my phD, I evaluated the ability of aminoglycosides and PTC124 to induce readthrough of premature termination codons, targeting and function of nonsense and missense mutants of Bsep and also the effect of combined therapy (readthrough + chaperone).In our expermental models, gentamicin increased readthrough of p.R1090X mutation NIH3T3, HEK293 and Can 10 lines. The resulting full-length protein was detected at the plasma membrane of HEK293 and at the canalicular membrane of Can 10 cells; and was partially functional since it was responsible for increasing the transport activity of 3H-taurocholate (3H-TC) in MDCK clones. These effects were potentiated by the addition of chaperone drugs such as 4-phenylbutyrate (4-PB).I have also demonstrated the ability of new 4-PB derived compounds (MHMPB, OTNC and HMPB) to correct mistrafficking and to increase 3H-TC transport of BsepR1128C missense mutant at lower concentrations than 4-PB. Finally, I showed that other chaperone drugs (GPB, PA, SAHA, and C18) were able to correct mistrafiking of BsepR1128C and to increase its 3H-TC transport activity in MDCK clones.

Indiana University-Purdue University Indianapolis (IUPUI) / Enteric viruses are among the most common infectious human viruses worldwide, causing an estimated 10-15 million infections per year in the United States. Among enteric viruses, Coxsackievirus is commonly isolated and can lead to the development of meningitis, encephalitis, pancreatitis, and hepatitis. Furthermore, Coxsackievirus B3 is the primary cause of viral myocarditis and can lead to pleurodynia, with nearly 40,000 symptomatic cases reported in the United States each year. The enteroviral ssRNA genome contains a 5’ untranslated region (5’UTR) which consists of two structural components, the cloverleaf and the internal ribosome entry site (IRES), both shown to be integral to viral success. Additionally, the viral genome encodes four structural VP proteins as well as 11 non-structural proteins. Polymorphisms found within the CVB3 population have been linked to viral virulence. Here, we compare two CVB3 Nancy variants to elucidate the downstream effects observed in response to mutations found in the CVB3 genome. Implementing our novel oral inoculation model, we aimed to determine the impact mutations found in the 5’UTR and VP regions exert on viral pathogenesis. We also aimed to delineate the in vitro effects of the observed mutations. We investigated the role mutations found in the structural regions played in virus host cell attachment, in vitro cell viability, and replication. Our work has further confirmed the relevance and impact of mutations found in the VP region of the CVB3 genome.

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