Graduation date: 1992

Undergraduate honors paper--Mount Holyoke College, 2005. Dept. of Chemistry. / Includes bibliographical references (leaves 107-111).

No description available.

Ultraviolet light damages genomic material by inducing the formation of covalent bonds between adjacent pyrimidines. Cis-syn cyclobutane pyrimidine dimers (CPD)constitute the most abundant primary lesion in DNA. Photolyase, a light-activated enzyme, catalytically repairs these lesions. Although many steps in the photolyase-mediated repair process have been mapped, details of the mechanism remain cryptic. Difference FT-IR spectroscopy was employed to obtain new mechanistic information about photorepair. Purified oligonucleotides, containing a central diuracil, dithymidine, or cyclobutane thymidine dimer, were monitored using vibrational methods. Construction of difference infrared data between undamaged and damaged DNA permitted examination of nucleic acid changes upon formation of the CPD lesion; these experiments indicated that C=O and C-H frequencies can be used as markers for DNA damage. Furthermore, in purified photolyase containing isotopically-labeled aromatic amino acids, we observed that tryptophan residues in photolyase underwent structural changes during photorepair. These data indicate that electron transfer during DNA repair occurs through-bond, and that redox-active, aromatic residues form the pathway for electron transfer. / Master of Science

Thesis (PhD (Molecular Biology and Human Genetics))--University of Stellenbosch, 2005. / 157 leaves single sided printed, preliminary pages i-xvii and numbered pages 1-141. Includes bibliography, and abbreviations and a list of figures. / ENGLISH ABSTRACT: A gene coding for Arylaminie N-acetyltransferase (NAT) has been found in Mycobacterium tuberculosis, the casual agent of tuberculosis (TB). N-acetyltransferase acetylates and inactivates isoniazid (INH), which is a front line drug used in TB therapy. A guanine to adenine SNP at basepair 619 (G619A) has previously been identified in this gene, which results in a glycine to arginine change at amino acid 207 (G207R) (Upton et al. 2001). In this study the nat gene was further characterised. The frequency of the G619A SNP was analysed in 37 M tuberculosis strain families found in the Western Cape Province of South Africa, and it was found that the G619A SNP is conserved in two strain families (strain family 3 and strain family 28). Further sequence analysis identified a new thymine to cytosine SNP at base-pair 529 (T529C) resulting in a tyrosine to histidine change at amino acid 177 (Yl77H). This SNP was found only in isolates from strain family 3. These results imply that these SNPs may be used in epidemiology studies to classify isolates into these strain families. Using Real Time PCR, the expression of nat in M bovis BCG and M tuberculosis (reference strain H37Rv) was determined over a 7 and 28 day growth cycle, respectively. Using 16S rRNA as an endogenous control, the nat gene was shown to be expressed early during the growth curve and reach its maximum expression level at approximately mid-log phase. The expression of nat was induced in drug susceptible M tuberculosis isolates (reference strain H37Rv and isolate 1430 containing both SNPs) exposed to INH at a concentration of O.Oll-lg/ml, but minimal change in expression was observed in resistant isolates (isolate 816) exposed to INH at the same concentration. Mycobacterium bovis BCG cultures exposed to INH, at a final concentration of 0.28I-lg/ml, showed an increase in protein production. The increase of nat mRNA and NAT protein in M tuberculosis and M bovis BCG, respectively, implies that INH affects the expression of NAT. The NAT protein was localised to all fractions of the cell in Mycobacterium smegmatis, M bovis BCG and M tuberculosis, using the Western blot technique. However, protein fractions from the cell envelope region showed a protein (detected with specific NAT antibodies) that ran at a higher molecular weight (MW). This implies that the cytosolic hydrophilic NAT undergoes some type of post-translational process that may make it hydrophobic, and enable it to pass into the cell envelope region. These results show for the first time how nat is expressed during the entire growth cycle of M tuberculosis and M. bovis BeG. It was shown that nat is expressed early during the growth cycle of the bacterium reaching maximum expression levels at mid-log phase. These results are in concordance with those obtained using M. smegmatis nat mutants, which taken together, show that early expression of nat is important for early growth and development of mycobacteria. The results in this study also showed that NAT appeared to be translocated into the cell envelope of the bacterium, implying that NAT may be involved in one of the pathways needed for complete formation of the cell envelope. These results suggest that NAT may be an important target for drug development, as inhibitors of NAT could result in hindered growth and hence spread of the bacterium within its host. Inhibitors may also result in the incomplete development of the cell wall, enabling the host to combat the disease using its own immune system.

The objectives of this work are to characterize and model the solvent-mediated phase transformation process of theophylline anhydrous crystals to the monohydrate crystals in an aqueous system. In order to model the transformation, the following processes are taken into account: (1) the dissolution kinetics of theophylline anhydrous crystals, (2) the kinetics of the formation of theophylline monohydrate nuclei, and (3) the growth kinetics of the monohydrate crystals. The driving forces for the above processes are determined from the concentration of theophylline in the solution and the solubilities of theophylline anhydrous and monohydrate. The solubilities of theophylline anhydrous and the monohydrate, and these three distinct processes along with the overall transformation phenomena were investigated in the present study. By using theophylline as a model compound we have gained some understanding of the kinetics of the solvent-mediated phase transformation between the metastable anhydrous form and the stable hydrated form of an organic compound and we were able to model the transformation process. By identifying the mechanisms for nucleation, growth of the hydrate form and the dissolution of the anhydrous form one can predict and control the transformation process. The growth kinetics of thymine monohydrate crystals at various temperatures are also investigated in the present study.

La tesis doctoral está dividida en 3 partes:La primera presenta la aplicación del grupo TCP a la síntesis de PNAs en fase sólida. La segunda está dedicada a la síntesis de un nuevo tipo de nucleoaminácido para la síntesis de nuevos nucleopéptidos. La tercera está centrada en los estudios iniciales de síntesis de derivados de Pantocina B, un compuesto con propiedades antimicrobianas. / The doctoral thesis is divided in 3 parts: The first presents the application of the TCP group to the synthesis of PNAs in solid phase. The second is dedicated to the synthesis of a new type of nucleoaminácid for the synthesis of new nucleopéptids. The third is centered in the initial studies of synthesis of derivatese of Pantocina B, a componend with antimicrobial properties.

The E3 ubiquitin ligase \(CRL4^{Cdt2}\) targets proteins for destruction during DNA replication and following DNA damage (Havens and Walter, 2011). Its substrates contain "PIP degrons" that mediate substrate binding to the processivity factor PCNA at replication forks and damage sites. The resulting PCNA-PIP degron complex forms a docking site for \(CRL4^{Cdt2}\), which ubiquitylates the substrate on chromatin. Several \(CRL4^{Cdt2}\) substrates are known, including Cdt1, multiple CDK inhibitors, Drosophila E2f1, human Set8, S. pombe Spd1, and C. elegans \(Pol\eta\) (Havens and Walter, 2011). An emerging theme is that \(CRL4^{Cdt2}\) targets proteins whose presence in S phase is toxic. Here, I used Xenopus egg extract to characterize a new \(CRL4^{Cdt2}\) substrate, thymine DNA glycosylase (TDG). TDG is a base excision repair protein that targets G-U and G-T mispairs, which arise from cytosine and 5-methylcytosine deamination (Cortazar et al., 2007). Thus, TDG may function in epigenetic gene regulation via DNA demethylation, in addition to its canonical DNA repair function. A yet unknown E3 ubiquitin ligase triggers TDG destruction during S phase (Hardeland et al., 2007). Understanding TDG proteolysis in S phase is relevant to the regulation of DNA replication, DNA repair, and epigenetic control of gene expression. I discovered that TDG contains a variant of the "PIP degron" consensus and that TDG is ubiquitylated and destroyed in a PCNA-, Cdt2-, and degron-specific manner during DNA repair and DNA replication in Xenopus egg extract. I further characterized what features of TDG contribute to its proteolysis. Interestingly, I could not identify any defects during DNA replication or during Xenopus embryonic development in response to a non-degradable form of TDG. Additionally, I examined how interactions between \(CRL4^{Cdt2}\) and multiple subunits of the PCNA homotrimer contribute to \(CRL4^{Cdt2}\) function. In a popular model, PCNA functions as a "tool belt" on DNA, binding three separate proteins through its individual subunits to facilitate rapid exchange of DNA replication and repair proteins as they are needed on DNA. To address this model, I generated a single chain polypeptide with three PCNA subunits connected through flexible linker sequences. I used this tool to determine how multiple PCNA subunits contribute to \(CRL4^{Cdt2}\) function. I found that a single wildtype subunit is sufficient for modest destruction of the \(CRL4^{Cdt2}\) substrate Cdt1, but complete Cdt1 destruction requires two separate wildtype subunits. Additionally, a single subunit was sufficient for leading strand elongation, challenging the "tool belt" model during DNA replication. I also discuss implications and future use of the single-chain PCNA.

Orientadores: João Ernesto de Carvalho, Ana Lucia Tasca Gois Ruiz / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-09T11:07:54Z (GMT). No. of bitstreams: 1 Monteiro_KarinMaia_M.pdf: 2254231 bytes, checksum: 20b2ee4f5d5aaf0109e94552d1fec08d (MD5) Previous issue date: 2006 / Resumo: O complemento nutricional ¿TK3¿ foi inicialmente estudado por um bioquímico alemão, Sr. Friedrich Lavitcshka, que desenvolveu uma formulação em 1969, inicialmente líquida, constituída basicamente pela associação de triptofano e timina. Seus estudos em modelos experimentais de tumores de pele induzidos por alcatrão em ratos não foram publicados. Entretanto, seus resultados, bem como relatos de casos provenientes do uso informal de tal suplementação, apontavam para efeitos benéficos superiores ao de um mero complemento nutricional ou ¿fortificante¿, como se costumava denominar tal categoria de substâncias. A avaliação toxicológica deste complemento, como parte inicial deste estudo pré-clínico, revelou: 1. Estudos ¿in vitro¿: atividade não citotóxica de ¿TK3¿ em cultura de células humanas normais ¿ fibroblastos ¿ e tumorais; 2. Estudos agudos ¿in vivo¿: a administração aguda de ¿TK3¿ (5 g/Kg, p.o. e 2g/Kg, i.p.) em ratos Wistar não produziu quaisquer sinais clínicos de toxicidade. A análise macroscópica dos órgãos destes animais experimentais não revelou quaisquer alterações sugestivas de toxicidade; 3. Estudos sub-crônicos ¿in vivo¿: a administração doses-repetidas 90 dias de ¿TK3¿ (100 mg/Kg, 300 mg/Kg e 1000 mg/Kg, p.o.) em ratos Wistar de ambos os sexos igualmente não revelou quaisquer sinais de toxicidade, confirmados pela análise macroscópica dos órgãos. Finalmente, as análises hematológicas e bioquímicas não identificaram alterações indicativas de toxicidade. A triagem farmacológica deste complemento revelou: 1. Em modelo de úlcera induzida por etanol em ratos , o tratamento com ¿TK3¿ (1000 mg/Kg, p.o.) reduziu o índice de lesão ulcerativa (86.2%). Esta atividade antiulcerogênica foi superior àquela apresentada pela administração dos componentes isoladamente (triptofano: 400mg/Kg [61.5%] e timina: 400 mg/Kg [+30.8%]); 2. Na avaliação da atividade antisecretora, em modelo de ligadura de piloro por 4 horas, a administração intraduodenal de ¿TK3¿ (1000 mg/Kg, p.o.) não reduziu o volume, nem a acidez total e nem aumentou o pH da secreção ácida gástrica basal; 3. Na triagem dos mecanismos de citoproteção gástrica, o pré-tratamento de ratos com indometacina (5 mg/Kg, p.o.) não inibiu o efeito protetor do ¿TK3¿ (1000 mg/Kg, p.o.) nas lesões induzidas por etanol; 4. O pré-tratamento de ratos com L-NAME (5 mg/Kg, i.v.) não inibiu o efeito protetor do ¿TK3¿ (1000 mg/Kg, p.o.) nas lesões induzidas por etanol; 5. Finalmente, o pré-tratamento de ratos com NEM (10 mg/Kg, s.c.) foi capaz de inibir em 50% o efeito protetor do ¿TK3¿ (1000 mg/Kg, p.o.) nas lesões induzidas por etanol, sugerindo a participação de compostos contendo grupos sulfidrila no mecanismo de ação do referido complemento / Abstract: The nutritional supplement ¿TK3¿ was originally studied by a German biochemist, Mr. Friedrich Lavitcshka, who first associated L-tryptophan and thymine, in a liquid formula, in 1969. His early studies using experimental tar-induced skin cancer models were not published even though they seemed to confirm the benefits reported by informal use of such association at that time. These reports suggested some pharmacological effects beyond the nutritional one. The toxicological evaluation of this new association of substances, as part of its pre-clinical trial, revealed: 1. ¿In vitro¿ studies: no citotoxicity activity of ¿TK3¿ on normal (fibroblasts) and cancer human cells; 2. ¿In vivo¿ acute studies: acute administration of ¿TK3¿ (5 g/Kg, p.o. and 2g/Kg, i.p.) in Wistar rats revealed no signs of systemic toxicity or impending death; 3. ¿in vivo¿ sub-chronic studies: 90 day repeated-dose study of ¿TK3¿ (100 mg/Kg, 300 mg/Kg and 1000 mg/Kg, p.o.) in Wistar rats of both sexes revealed no clinical signs of toxicity, confirmed by both histopathological and biochemical analysis. The pharmacological screening of this nutritional supplement revealed: 1. In the ethanol-induced gastric ulcer experimental model in rats, the treatment with ¿TK3¿ (1000mg/Kg, p.o.) reduced the ulcerative ulcer index (86.2%). This antiulcerogenic activity was superior to the ones presented by the isolated components administrated individually (L-tryptophan: 400mg/Kg [61.5%] and thymine: 400mg/Kg [+30.8%]); 2. In the evaluation of gastric secretion through pyloric ligation model in rats, the treatment with ¿TK3¿ (1000 mg/Kg, i.d.) had no significant effect over the gastric juice volume, nor the pH or hydrogenionic concentration of gastric content; 3. In the evaluation of possible gastric cytoprotective mechanisms of action, pre-treatment of experimental rats with indomethacin (5 mg/Kg, p.o.) did not inhibit the antiulcerogenic effect of ¿TK3¿ (1000 mg/Kg, p.o.) in the ethanol induced ulcer model; 4. Similarly, pre-treatment of experimental rats with L-NAME (5 mg/Kg, i.v.) did not inhibit the antiulcerogenic effect of ¿TK3¿ (1000 mg/Kg, p.o.) in the ethanol induced ulcer model; 5. Finally, pre-treatment of experimental rats with NEM (10 mg/Kg, s.c.) decreased 50% of the antiulcerogenic effect of ¿TK3¿ (1000 mg/Kg, p.o.) in the ethanol induced ulcer model, suggesting the participation of endogenous non-protein SH-containing compounds. However, as this reduction was not complete, there seems to be more aspects involved in this mechanism of action / Mestrado / Ciencias Basicas / Mestre em Clinica Medica

When the thymine base is oxidized, the resulting cation may deprotonate reversibly at N3, or irreversibly at >C5-CH3. In all thymine derivatives studied so far in the solid state, there is always a significant concentration of a radical formed by net H-abstraction from the >C5-CH 3. DFT calculations on this allyl-like radical are in good agreement with the experimental results for both the isotropic and anisotropic hyperfine couplings. There is a tendency for the thymine cation to deprotonate at N3 in solution. Calculations on the N3 deprotonated thymine cation yield two structures, one planar radical with an unusually large N1-C2 bond length, and one nonplanar radical with the N3 more than 25° out of the molecular plane. Calculations show that the structure with the lowest energy is the allyl-like radical.