The ability to synthesize pyrimidine nucleotides is essential for most organisms. Pyrimidines are required for RNA and DNA synthesis, as well as cell wall synthesis and the metabolism of certain carbohydrates. Recent findings, however, indicate that the pyrimidine biosynthetic pathway and its intermediates maybe more important for bacterial metabolism than originally thought. Maksimova et al., 1994, reported that a P. putida M, pyrimidine auxotroph in the third step of the pathway, dihydroorotase (DHOase), failed to produce the siderophore pyoverdin. We created a PAO1 DHOase pyrimidine auxotroph to determine if this was also true for P. aeruginosa. Creation of this mutant was a two-step process, as P. aeruginosa has two pyrC genes (pyrC and pyrC2), both of which encode active DHOase enzymes. The pyrC gene was inactivated by gene replacement with a truncated form of the gene. Next, the pyrC2 gene was insertionally inactivated with the aacC1 gentamicin resistance gene, isolated from pCGMW. The resulting pyrimidine auxotroph produced significantly less pyoverdin than did the wild type. In addition, the mutant produced 40% less of the phenazine antibiotic, pyocyanin, than did the wild type. As both of these compounds have been reported to be vital to the virulence response of P. aeruginosa, we decided to test the ability of the DHOase mutant strain to produce other virulence factors as well. Here we report that a block in the conversion of carbamoyl aspartate (CAA) to dihydroorotate significantly impairs the ability of P. aeruginosa to affect virulence. We believe that the accumulation of CAA in the cell is the root cause of this observed defect. This research demonstrates a potential role for pyrimidine intermediates in the virulence response of P. aeruginosa and may lead to novel targets for chemotherapy against P. aeruginosa infections.

The purpose of this investigation is to study the effects of methylxanthines, catecholamines, and cyclic nucleotides on melanin synthesisand conidiation using the technique of phase contrast microscopy. Verticillium wild type (T9) strain was grown in both sucrose nitrate liquid medium and polygalacturonic acid media (SNLM and PGAM). These media allowed rapid production of conidia and synchronous development of microsclerotia respectively. Even though caffeine has a greater effect on conidiation, both caffeine and theophylline promoted melanization. Dibutyl cyclic AMP to lesser extent inhibited conidiation, while cyclic AMP had little to no effect on conidiation. Dibutyl cyclic AMP inhibited melanin production. Cyclic AMP had a stimulatory effect on melanin production. Isoproterenol a stimulant of adenylate cyclase activity, inhibited conidiation the first two days, but had no apparent effect after day 3. Isoproterenol also induced melanin production in the flask. Propranolol, an antagonist of hormonally induced adenylate cyclase activity, did not repress conidiation when compared to the drug-free SNLM. Melanin was not formed in either SNLM and PGAM, suggesting that the effect of propranolol was opposite that of isoproterenol. Propranolol, a beta blocking agent, reversed the isoproterenol induced inhibition of conidiation. This reversal indicates that there is a receptor which isoproterenol attached itself to - the binding beta receptor site. The isoproterenol effect on conidiation and melanin synthesis indicates that, there might be cyclic AMP involvement in development, since this agent affects cyclic AMP level. Since melanin is known to be associated with microsclerotia, it is possible that cyclic AMP might be involved in this development. In this study, the effects of methylxanthines, catecholamines and cyclic nucleotides on melanin synthesis and conidiation was determined. There is every possibility that cyclic AMP might be involved in the regulation of conidiation process and melanin synthesis.

Aspartate transcarbamoylase (ATCase) catalyzes the first committed step in pyrimidine biosynthesis. Bacterial ATCases are divided into three classes, A, B and C. Class A ATCases are largest at 450-500, are. dodecamers and represented by Pseudomonas ATCase. The overlapping pyrBC' genes encode the Pseudomonases ATCase, which is active only as a 480 kDa dodecamer and requires an inactive pyrC'-encoded DHOase for ATCase activity. ATCase has been studied in two non-pathogenic members of Mycobacterium, M. smegmatis and M. phlei. Their ATCases are dodecamers of molecular weight 480 kDa, composed of six PyrB and six PyrC polypeptides. Unlike the Pseudomonas ATCase, the PyrC polypeptide in these mycobacteria encodes an active DHOase. Moreover, the ATCase: DHOase complex in M. smegmatis is active both as the native 480 kDa and as a 390 kDa complex. The latter lacks two PyrC polypeptides yet retains ATCase activity. The ATCase from M. phlei is similar, except that it is active as the native 480 kDa form but also as 450,410 and 380 kDa forms. These complexes lack one, two, and three PyrC polypeptides, respectively. By contrast,.ATCases from pathogenic mycobacteria are active only at 480 kDa. Mycobacterial ATCases contain active DHOases and accordingly. are placed in class A1 . The class A1 ATCases contain active DHOases while class A2 ATCases contain inactive DHOases. ATCase has also been purified from Burkholderia cepacia and from an E. coli strain in which the cloned pyrB of B. cepacia was expressed. The B. cepacia ATCase has a molecular mass of 550 kDa, with two different polypeptides, PyrB (52 kDa) and PyrC of (39 kDa). The enzyme is active both as the native enzyme at 550 kDa and as smaller molecular forms including 240 kDa and 165 kDa. The ATCase synthesized by the cloned pyrB gene has a molecular weight of 165 kDa composed of three identical PyrB and no PyrC polypeptides. Nucleotide effectors ATP, CTP, and UTP inhibited all forms of enzymes. Because of its size and its activity as a trimer and smaller than native forms, the B. cepacia enzyme is placed in a new class.

The glyoxalase system mediates the conversion of methylglyoxal, a toxic ketoaldehyde, to D-lactic acid. The system is composed of two enzymes, glyoxalase I (Glo-I) and glyoxalase II (Glo-II), and exhibits an absolute requirement for a catalytic quantity of glutathione (GSH). Glo-I catalyzes the isomerization of a hemithioacetal, formed non-enzymatically from methylglyoxal and GSH, to the corresponding a -D-hydroxyacid thioester, s-D-lactoylglutathione (SLG). Glo-II catalyzes the irreversible breakdown of SLG to D-lactate and GSH. We have observed that ATP or GTP significantly inhibits the Glo-II activity of tissue homogenates from various sources. We have developed a rapid, one step chromatography procedure to purify Glo-II such that the purified enzyme remains "sensitive" to inhibition by ATP or GTP (Glo-II-s). Studies indicate that inhibition of Glo-II-s by nucleotides is restricted to ATP, GTP, ADP, and GDP, with ATP appearing most effective. Kinetics studies have shown that ATP acts as a partial non-competitive inhibitor of Glo-II-s activity, and further suggest that two kinetically distinguishable forms of the enzyme exist. The sensitivity of pure Glo-II-s to nucleotide inhibition is slowly lost on storage even at -80° C. This loss is accelerated at higher temperatures or in the presence of ATP. Kinetics studies on the resultant "insensitive" enzyme (Glo-II-i) show that a significant reduction of the affinity of the enzyme for the substrate, SLG, occurs and further suggest that only one form of the enzyme is kinetically distinguishable after "de-sensitization". Tryptophan fluorescence studies of the two enzyme preparations suggest that a subtle conformational change in the enzyme has occurred during de-sensitization. We have also observed that Glo-II-i is "resensitized" to nucleotide inhibition after incubation in the presence of a reagent that reduces disulfide bonds. The resensitized enzyme exhibits an increased KM value similar to that of the original Glo-II-s. Kinetics studies show that ATP or GTP again act as partial non-competitive inhibitors of the resensitized enzyme and suggest that only one form of the enzyme is present. The physiological significance of the two enzyme forms is discussed.

In this research, the necessity of understanding and using bioinformatics is demonstrated using the enzyme aspartate transcarbamoylase (ATCase) as the model enzyme. The first portion of this research focuses on the use of bioinformatics. A partial sequence of the pyrB gene found in Enterococcus faecalis was submitted to GenBank and was analyzed against the contiguous sequence from its own genome project. A BLAST (Basic Local Alignment Search Tool; Atschul, et al., 1990) was performed in order to hypothesize the remaining portion of the gene from the contiguous sequence. This allowed a global comparison to other known aspartate transcarbamoylases (ATCases) and once deduced, a translation of the sequence gave the stop codon and thus the complete sequence of the open reading frame. When this was complete, upstream and downstream primers were designed in order to amplify the gene from genomic DNA. The amplified product was then sequenced and used later in phylogenetic analyses concerning the evolution of ATCase. The second portion of this research involves taking multiple ATCase nucleotide sequences and performing phenetic and phylogenetic analyses of the archaea and eubacter families. From these analyses, ancestral relationships which dictate both structure and function were extrapolated from the data and discussed.

Changes in myocardial energetics have been implicated in the pathophysiology of heart failure (HF). However, the precise contribution of creatine (Cr) / phosphocreatine (PCr) / creatine kinase (CK) energy buffer and transfer remains unclear. The aim of this thesis was to study the effects on murine cardiac function of both impairment and enhancement of creatine metabolism. In order to longitudinally follow the cause and effect relationship of myocardial creatine concentration, a non-invasive method of quantification was required. Cardiac Cr levels measured in vivo by 1H-MRS were therefore compared with gold-standard invasive HPLC and found to correlate over a wide-range (r2=0.91). 1H-MRS was reproducible for measuring Cr levels in the heart, brain, and skeletal muscle. The cardiac phenotype of a novel model of creatine depletion, the AGAT-/- mouse, was characterized using in vivo MRI, 1H-MRS and LV catheterisation, under conditions of gradually reducing Cr concentrations; zero Cr; and attempted phenotype rescue with dietary Cr. For the first time in the heart, the rate of Cr turnover was quantified (~3 % per day) and demonstrated that cardiac function was preserved even when creatine levels reduced by ~70-90%. Total absence of myocardial Cr induced impairment of inotropic and lusitropic cardiac function and reduced inotropic reserve. Cardiac dysfunction was only partially rescued by replenishment of the Cr pool, suggesting this to be a consequence of long-term adaptations to chronic low Cr. Finally, we tested the hypothesis that combined elevation of myocardial creatine and ribose would be beneficial in a mouse model of chronic HF by increasing cardiac energy availability. Despite an increase in myocardial ribose concentration, this did not prevent loss of total adenine nucleotides (TAN), and there was no improvement in post-infarct LV remodeling or function. Future studies are needed to explore alternative approaches for maintaining TAN in combination with total creatine.

Like its enteric counterpart, aspartate transcarbamoylase (ATCase) from Pseudomonas putida is a dodecamer of two different polypeptides. Unlike the enterics, the Pseudomonas ATCase lacks regulatory polypeptides but employs instead inactive dihydroorotases for an active dodecamer. Previous work showed that PyrB contains not only the active site but also the effector binding sites for ATP, UTP and CTP at its N-terminus. In this work, 11 amino acids were deleted from the N-terminus of PyrB and the ATCase with the truncated protein was expressed in E. coli pyrB- and purified. The wild type enzyme was similarly treated. Velocity-substrate plots without effectors gave Michaelis-Menten kinetics in all cases. Deleting 11 amino acids did not affect dodecameric assembly but altered effector responses. When carbamoylphosphate was varied, the mutant enzyme was inhibited by UTP while the wild type enzyme was activated 2-fold. When the aspartate was varied, CTP had no effect on the mutant enzyme but strongly inhibited the wild type enzyme.

La squalénisation est une méthode de vectorisation sous forme nanoparticulaire qui consiste àcoupler de manière covalente un dérivé du squalène à des principes actifs hydrophiles tels que lesanalogues nucléosidiques. Les conjugués amphiphiles obtenus sont capables de s’auto-organiserspontanément dans l’eau en nanoparticules d’une centaine de nanomètres de diamètre etpossèdent des activités anticancéreuses ou antivirales remarquables. Notre objectif était d’étendrecette stratégie à différentes classes d’antitumoraux, comme les antimétabolites, les antimitotiqueset les agents alkylants. Différents dérivés du squalène ont ainsi été synthétisés puis couplés à cesprincipes actifs pour former les bioconjugués squalénisés correspondants. Il a été montré que cesprodrogues étaient capables de s’auto-assembler en nanoparticules spontanément en milieuaqueux, que le principe actif soit hydrophile ou hydrophobe. Les suspensions nanoparticulaires deces prodrogues se sont montrées actives in vitro sur différentes lignées cellulaires cancéreuseshumaines et murines et in vivo chez la Souris sur des modèles de cancer. La squalénisation a donc étéétendue à diverses familles de composés anticancéreux confirmant qu’il s’agit d’une méthodegénérale de vectorisation pourvue d’un fort potentiel thérapeutique. / Squalenoylation is a strategy of vectorization consisting in coupling squalene derivatives tohydrophylic drugs as nucleoside analogues. The amphiphilic conjugates obtained are able to selfassembleinto nanoparticles with a diameter of 100 nm in water. In addition those nanoparticleshave shown impressive anticancer and antiviral activities. Our objective was to extend this strategyto different anticancer drugs as antimetabolites, antimitotics and alkylating agents. Differentsqualenoyl derivatives have been synthesised and then coupled to drugs to furnish thecorresponding squalenoylated biconjugates. It has been shown that those prodrugs were able toself-assemble into nanoparticles in water. Nanoparticles of the bioconjugates are active in vitro ondifferent human cancer cell lines and in vivo in Mice on different cancer models. Squalenoylation hasfinally been extended to numerous anticancer drugs, proving that this strategy is a general methodof vectorization with a high therapeutic potential.

O objetivo deste trabalho foi avaliar a utilização da levedura hidrolisada como fonte de nucleotídeos para frangos de corte. As aves foram suplementadas com diferentes níveis de inclusão nas dietas iniciais de 1 a 14 dias de idade. Foram utilizados um total de 576 pintos da linhagem Ross 708, os quais foram distribuídos em 6 tratamentos com 8 repetições (12 aves por box). Os tratamentos consistiram da inclusão de 0, 2, 4, 6, 8 e 10 kg de levedura hidrolisada/tonelada de ração. A levedura hidrolisada foi adicionada na dieta no lugar do material inerte da ração. A dieta inicial foi fornecida na forma triturada enquanto as dietas de crescimento, final e de retirada foram fornecidas na forma de pellets. Durante todo o experimento o acesso à água e ração foi ad libitum. Todas as dietas foram feitas à base de milho, farelo de soja e gordura de frango e foram formuladas para atender as exigências nutricionais recomendadas pelo manual de recomendações nutricionais Ross 708. Aos 42 dias, as aves alimentadas com 1% de levedura hidrolisada tiveram maior peso corporal e ganho de peso quando comparadas aos demais tratamentos (P<0,05). Não houveram diferenças estatísticas entre os tratamentos para as variáveis mortalidade e densidade de vilos. Contudo aves que não foram suplementadas com levedura hidrolisada (tratamento controle) apresentaram menor profundidade de cripta e a suplementação de 1% de levedura resultou em maior altura de vilos. Aves as quais receberam dietas com 0,2% de inclusão de levedura hidrolisada apresentaram menor rendimento de peito que as aves que receberam os demais níveis de levedura, mas foram iguais as aves do tratamento controle. Contudo, o rendimento de carcaça, sassami e gordura abdominal não foram influenciados pelos tratamentos experimentais. Estes resultados demostraram a eficácia da utilização de levedura hidrolisada na dieta de frangos de corte no período de 1 a 14 dias sobre as características de produção. / The objective of this work was to evaluate hydrolyzed yeast utilization as nucleotides source to broilers. Birds were supplemented with different inclusion levels on starter diets from 1 to 14 days of age. A total of five hundred seventy six Ross 708 chicks were allotted to 6 experimental treatments with 8 replications (12 broilers per pen). Birds were randomly distributed in following treatments: 0, 2, 4, 6, 8 and 10 kg hydrolyzed yeast/ton of feed. Hydrolyzed yeast was added to the test diet in place of filler. Starter diets were supplied in crumbled form while grower, finisher, and withdrawal were supplied in pellet form. Throughout experiment water and feed were supplied ad libitum. All diets were based on corn, soybean meal and poultry fat, and were formulated to achieve nutritional requirements from recommendations guide for Ross x Ross 708 broilers. At 42 d chicks fed 1% hydrolyzed yeast demonstrated higher body weight and body weight gain over birds fed other treatments (P<0.05). Mortality and villous density did not differ among treatments. However birds fed control treatment showed lower crypt depth and 1% hydrolyzed yeast supplementation promoted higher villous high. Birds fed 0.2% hydrolyzed yeast showed lower breast meat yield than birds received other yeast levels, but were equals to control treatment control. However, carcass and tender yield, and abdominal fat were not influenced by treatments. These results indicated efficacy of hydrolyzed yeast utilization on broiler diets from 1 to 14 on production characteristics.

O avanço tecnológico dos laboratórios de biologia molecular tem proporcionado um grande aumento no volume de seqüências de nucleotídeos armazenadas em bancos de dados biológicos, introduzindo o desafio de pesquisar eficientemente estes dados. Neste contexto, a árvore de sufixo é um método de acesso utilizado por muitas aplicações que envolvem pesquisa em dados biológicos. Entretanto, o custo de construção das árvores de sufixo é alto devido ao tamanho da estrutura de indexação gerado e à necessidade da árvore de sufixo caber em memória principal para ser construída com complexidade linear em relação ao tempo. Esta dissertação propõe o Perseus, uma nova técnica para tratar árvores de sufixo persistentes. A técnica Perseus apresenta os seguintes diferenciais. Ela introduz uma abordagem que realiza a construção de árvores de sufixo persistentes cujos tamanhos podem exceder a capacidade da memória principal. Além disso, ela provê um algoritmo que constrói árvores de sufixo por meio do particionamento destas árvores somente quando necessário. Esta construção também permite que o usuário escolha quais subseqüências de uma seqüência devem ser indexadas, de acordo com os requisitos particulares de suas aplicações. Por fim, a técnica proposta também introduz um algoritmo de casamento exato que permite a busca por uma seqüência de consulta em árvores de sufixo que podem estar particionadas. A validação do Perseus foi realizada por meio de testes de desempenho considerando genomas de vários organismos, os quais possuem diferentes ordens de magnitude de tamanho. Os resultados obtidos foram comparados com a técnica Trellis+, a qual representa o estado da arte nesta linha de pesquisa. Os testes indicaram que o Perseus construiu árvores de sufixo mais rapidamente do que o Trellis+, reduzindo o tempo total gasto na construção em até 24%. Perseus também criou árvores de sufixo mais compactas, atingindo uma redução média de 27% no espaço de memória secundária utilizado. Já com relação ao tempo total gasto no processamento de consultas, Perseus sempre produziu os melhores resultados, respondendo consultas em média 49% mais rápido do que o seu principal concorrente. Com relação à indexação de subseqüências escolhidas pelo usuário, comparando os resultados obtidos com o Trellis+, os testes mostraram que Perseus proveu uma redução no tempo de construção de árvores de sufixo de 97% na média e uma redução no tempo gasto no processamento de consultas de genes de 93% na média / Due to the technological advances in molecular biology laboratories, biological databases are extremely voluminous and tend to become more voluminous as data on new genome organisms are available. This introduces the challenge of searching nucleotide sequences efficiently. The suffix tree is an access method used for several applications that search for these data. However, the cost of building suffix trees is high, since they are extremely large data structures and they should fit in the main memory to be constructed in linear time. In this masters thesis, we propose the Perseus, a novel technique that handles persistent suffix trees. The Perseus introduces the following distinctive good properties. It is based on an approach that constructs persistent suffix trees whose sizes may exceed the main memory capacity. Furthermore, it provides an algorithm that allows for users to indicate which substrings of the input string should be indexed, according to the requirements of their applications. Moreover, it proposes an extended exact matching algorithm that searches for a query string into suffix trees that may be partitioned. The Perseus was validated through performance tests using genomes of several organisms of different sizes. The results were compared with the Trellis+ technique, which represents the state-of-the-art in this field. The tests showed that the Perseus reduced the time spent on constructing suffix trees by 24%. The Perseus also constructed compacter suffix trees, providing an average reduction in the secondary memory storage of 27%. Furthermore, the Perseus reduced the time spent on query processing of nucleotide sequences by up to 49%. As for the functionality of indexing substrings according to the users requirements, the Perseus greatly improved the query performance in comparison to the Trellis+. The results showed that the Perseus reduced the time spent on constructing suffix trees by 97% on average and the time spent on query processing of genes by 93% on average