Indiana University-Purdue University Indianapolis (IUPUI) / Thiamin diphosphate (ThDP)-dependent enzymes catalyze a wide range of reactions including the oxidative and nonoxidative decarboxylation of 2-keto acids, carboligation reactions, the cleavage of C-C bonds, and the formation of C-S, C-N, and C-O bonds. Surprisingly, given this diversity, all ThDP-dependent enzyme catalyzed reactions proceed through essentially the same intermediate. This suggests that these enzymes share a common ancestry and have evolved to become the diverse group of enzymes seen today. Sequence alignments have revealed that all ThDP-dependent enzymes share two common ThDP binding domains, the PYR domain and the PP domain. In addition to these conserved domains, over time, other domains have been added creating further diversity in this superfamily. For instance, the TH3 domain, found in many ThDP-dependent enzymes, serves the function of binding additional cofactors such as FAD in enzymes like acetohydroxyacid synthase (AHAS) but in others, like pyruvate decarboxylase (PDC), it has lost this function completely. The work presented here focuses on ThDP-dependent decarboxylases. In this thesis, several evolutionary aspects of this group of enzymes will be examined including (i) the characterization of an evolutionary forerunner in the presence of a mechanism-based inhibitor, (ii) the characterization of the minor isozymes of pyruvate decarboxylase from Saccharomyces cerevisiae, and (iii) the development of a selection method to increase the efficiency of the site-saturation mutagenesis used to study ThDP-dependent enzyme evolution.

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Polychlorinated biphenyls (PCBs) decrease thyroid function in rats and mice by inducing activity of a liver enzyme, uridine diphosphate-glucuronosyltransferase (UDP-GT), thereby increasing thyroxine (T4) clearance. This loss of T4 can lead to hypothyroidism. In this study, an assay was validated for measuring UDP-GT activity toward T4 in Japanese quail (Coturnix japonica). Then UDP-GT induction by Aroclor 1254 was evaluated in quail, and quail and mice were compared in their responses to Aroclor 1254. In Experiment 1, Japanese quail and Balb/c mice were dosed orally with vehicle or Aroclor 1254 (250 or 500 mg/kg) and sacrificed five days later. In Experiment 2, Japanese quail were dosed orally with vehicle or Aroclor 1254 (500 mg/kg) and sacrificed either five or 21 days later. Total liver UDP-GT capacity increased with Aroclor 1254 exposure in all treatment groups of both species. Enzyme induction led to a trend to decreased plasma T4 concentrations at both doses and exposure times in quail and significantly decreased plasma T4 concentrations at both doses in mice. PCBs altered thyroid function in quail, but they did not become hypothyroid. This was in contrast to mice, which did become hypothyroid. It is unclear how PCBs affect the hypothalamic-pituitary-thyroid (HPT) axis in quail, and activation of the HPT axis appears to be inhibited in mice. Overall, quail showed a lesser response than mice to equivalent doses of Aroclor 1254, so it appears that birds may be less vulnerable to PCBs than mammals. / Master of Science

Les propriétés physiques d'un matériau sont intimement liées à sa structure cristalline et dans le cas d'ions dopants aux sites qu'ils occupent. La première partie de ce travail est dédiée au matériau diphosphate de sodium et de zinc Na2ZnP2O7, cristallisé out vitreux et ceci pour les ions dopants Co2+, Ni2+, Mn2+ et Eu3+. Les phases cristallisées ont été obtenues par la méthode Czochralski, les verres par trempe à partir de l'état fondu. Un ensemble de caractéristiques physiques ont été mises en jeu (Raman, infrarouge, RPE, absorption optique, luminescence) pour déterminer les sites occupés par les ions dopants et l'influence sur les propriétés optiques. La deuxième partie de cet travail consiste à une meilleure connaissance des matériaux diélectriques sans plomb appartenant à la famille pérovskite et plus particulièrement à la solution solide NaNbO3-BaTiO3. Des monocistaux ont été obtenus par la méthode des flux et caractérisés en utilisant plusieurs techniques : diffraction X, microanalyse, évolution thermique des domaines ferroélectriques-ferroélastiques, mesures diélectriques, piézoélectriques et pyroélectriques.

Les peroxyrédoxines (PRXs) forment une famille de peroxydases communes à tous les organismes vivants et ubiquitaires dans la cellule. Leur particularité provient d’un ou deux résidus cystéines accomplissant un cycle d’oxydo-réduction à l’aide d’un donneur d’électron. Ces protéines thiols sensibles au potentiel redox sont impliquées dans le mécanisme de détoxification du H2O2, une molécule oxydante induite lors de situations de stress. Les PRXs pourraient être induites par le stress et régulées par phosphorylation. En effet, des expérimentations in vitro ont démontré que la nucléoside diphosphate kinase 1 (NDPK1) a la capacité de phosphoryler une PRX cytosolique de pomme de terre. Ce mémoire décrit les travaux expérimentaux effectués pour caractériser la fonction de la PRX. Pour cela, le clonage d’une isoforme a été effectué, suivi d’une caractérisation biochimique et d’une étude d’expression de la protéine. Les données de séquençage révèlent qu’il s’agit d’une PRX de type II phylogénétiquement liée aux PRXs cytosoliques. L’ADNc codant pour cette peroxyrédoxine (PRX1) a été cloné chez Solanum chacoense. Une protéine recombinante portant une étiquette (6xHis) en N-terminale a été produite. Des essais enzymatiques ont confirmé la fonction antioxydante de la protéine recombinante et un anticorps polyclonal a été généré chez le lapin puis utilisé en conjonction avec un anticorps anti-NDPK1 pour déterminer les patrons d’expression généraux de ces protéines chez Solanum lycopersicum et Solanum tuberosum lors de situations de stress. Les données démontrent que les deux protéines sont généralement co-exprimées mais pas co-régulées et que la PRX1 est induite en certaines situations de stress. / The peroxiredoxins (PRXs) are a recently discovered family of peroxidases found in all organisms and ubiquitous in the cell. An important particularity of these proteins is the presence of one or two active cysteines that accomplish an oxydo-reduction cycle with an electron donor. The PRXs are sensitive to the redox potential and are implicated in the detoxification of the H2O2, an oxidante molecule induced in stress situations. The PRXs should be induced in stress situations and regulated by phosphorylation. Indeed, in vitro experimentations have shown that the NDPK1 can phosphorylate a cytosolic PRX isoform of the potato. This dissertation describes the experimentation made to acquire a preliminary understanding of the function of the PRX. For this purpose, we cloned a PRX isoform, followed by a biochemical characterization and expression studies of the protein. The sequencing data shown a type II PRX phylogenetically related to the cytosolic isoforms. The cDNA of this peroxiredoxin (PRX1) has been cloned in Solanum chacoense. The recombinant protein produced had a N-terminal (6xHis) tag. Enzymatic assays confirmed the antioxidant activity of the recombinant protein and a polyclonal antibody has been generated from the rabbit. This antibody was used in conjunction with an antibody anti-NDPK1 to determine the general expression patterns of those proteins during stresses in Solanum lycopersicum and Solanum tuberosum. The results obtained showed that the two proteins are generally co-expressed but not co-regulated. Obvious experimental facts displayed an induction of the PRX1 in biotic and abiotic stresses situations.

Depuis peu, des travaux ont montré que chez l’Homme, la transcétolase (TK, EC 2.2.1.1.) dont le cofacteur est la thiamine diphosphate (forme active de la vitamine B1), est une enzyme impliquée dans de nombreuses maladies telles que, le diabète, certains cancers, ou encore des maladies neurologiques, comme le syndrome de Wernicke-Korsakoff et la maladie d’Alzheimer. Pour des applications thérapeutiques, des inhibiteurs spécifiques de cette enzyme sont actuellement conçus et synthétisés dans les milieux académiques et industriels. Afin de déterminer l’activité de la TK (dans un but de diagnostic) d’une part, et de détecter des inhibiteurs potentiels de cette enzyme (dans un but thérapeutique) d’autre part, il est nécessaire de disposer de tests alliant rapidité, sensibilité et faible coût. Nous avons envisagé d’utiliser des biocapteurs ampérométriques qui combinent l’ensemble de ces avantages, et qui, de plus, n’ont jamais été mis en oeuvre avec la TK. Pour la détermination de l’activité des TK d’E. coli et humaine libres en solution, nous avons tout d’abord élaboré un premier biocapteur à galactose oxydase (GAOx, EC 1.1.3.9), dans lequel cette enzyme est immobilisée sur la laponite. Puis, dans le but de detecter des inhibiteurs de la TK, avec un système réutilisable, nous avons developpé un biocapteur à GAOx-TK d’E. coli, les deux enzymes étant co-immobilisées à la surface de l’électrode. Pour cela la TK a été immobilisée dans des Hydroxydes Doubles Lamellaires (HDL). Ce biocapteur bicouche et bi-enzymatique GAOx-TK, nous a permis d’évaluer l’effet d’inhibiteurs, tels que différents analogues du cofacteur et de substrats pris comme modèles. / Some recent studies have shown that human transketolase (TK, EC 2.2.1.1.), which thiamine diphosphate (active form of vitamin B1) is the cofactor, is involved in numerous disease such as diabete, some cancers and neurodegenerative diseases as Alzheimer’s disease and Wernicke-Korsakoff syndrome. For therapeutic purposes, TK inhibitors have been designed and synthesized in both academic and industrial fields. To determine TK activity (diagnostic) on the one hand, and to detect potential inhibitors of this enzyme (therapeutic) on the other hand, it is necessary to develop fast, sensitive and low cost assays. In this context, we designed some original amperometric biosensors that combine these advantages and were never studied with TK from now. We performed a first galactose oxidase (GAOx, EC 1.1.3.9) biosensor for E. coli and human TK activities detection. For that purpose, GAOx was immobilized on laponite matrix. Then, we designed a GAOx-TK biosensor by co-immobilization of GAOX and TK on the electrode surface that enabled the detection TK inhibitors with a reusable system. Thence, TK was immobilized in Layered Double Hydroxides (HDL). This bilayer and bi-enzymic biosensors, allowed us to determine the inhibitor potencies of several cofactors and substrates analogues as model compounds.

Les peroxyrédoxines (PRXs) forment une famille de peroxydases communes à tous les organismes vivants et ubiquitaires dans la cellule. Leur particularité provient d’un ou deux résidus cystéines accomplissant un cycle d’oxydo-réduction à l’aide d’un donneur d’électron. Ces protéines thiols sensibles au potentiel redox sont impliquées dans le mécanisme de détoxification du H2O2, une molécule oxydante induite lors de situations de stress. Les PRXs pourraient être induites par le stress et régulées par phosphorylation. En effet, des expérimentations in vitro ont démontré que la nucléoside diphosphate kinase 1 (NDPK1) a la capacité de phosphoryler une PRX cytosolique de pomme de terre. Ce mémoire décrit les travaux expérimentaux effectués pour caractériser la fonction de la PRX. Pour cela, le clonage d’une isoforme a été effectué, suivi d’une caractérisation biochimique et d’une étude d’expression de la protéine. Les données de séquençage révèlent qu’il s’agit d’une PRX de type II phylogénétiquement liée aux PRXs cytosoliques. L’ADNc codant pour cette peroxyrédoxine (PRX1) a été cloné chez Solanum chacoense. Une protéine recombinante portant une étiquette (6xHis) en N-terminale a été produite. Des essais enzymatiques ont confirmé la fonction antioxydante de la protéine recombinante et un anticorps polyclonal a été généré chez le lapin puis utilisé en conjonction avec un anticorps anti-NDPK1 pour déterminer les patrons d’expression généraux de ces protéines chez Solanum lycopersicum et Solanum tuberosum lors de situations de stress. Les données démontrent que les deux protéines sont généralement co-exprimées mais pas co-régulées et que la PRX1 est induite en certaines situations de stress. / The peroxiredoxins (PRXs) are a recently discovered family of peroxidases found in all organisms and ubiquitous in the cell. An important particularity of these proteins is the presence of one or two active cysteines that accomplish an oxydo-reduction cycle with an electron donor. The PRXs are sensitive to the redox potential and are implicated in the detoxification of the H2O2, an oxidante molecule induced in stress situations. The PRXs should be induced in stress situations and regulated by phosphorylation. Indeed, in vitro experimentations have shown that the NDPK1 can phosphorylate a cytosolic PRX isoform of the potato. This dissertation describes the experimentation made to acquire a preliminary understanding of the function of the PRX. For this purpose, we cloned a PRX isoform, followed by a biochemical characterization and expression studies of the protein. The sequencing data shown a type II PRX phylogenetically related to the cytosolic isoforms. The cDNA of this peroxiredoxin (PRX1) has been cloned in Solanum chacoense. The recombinant protein produced had a N-terminal (6xHis) tag. Enzymatic assays confirmed the antioxidant activity of the recombinant protein and a polyclonal antibody has been generated from the rabbit. This antibody was used in conjunction with an antibody anti-NDPK1 to determine the general expression patterns of those proteins during stresses in Solanum lycopersicum and Solanum tuberosum. The results obtained showed that the two proteins are generally co-expressed but not co-regulated. Obvious experimental facts displayed an induction of the PRX1 in biotic and abiotic stresses situations.

Previous studies have shown that the formulation of an active pharmaceutical ingredient (API) entrapped in the Pheroid® (Pheroid for simplification) delivery system enhances absorption of the API, suppresses its metabolism, and may contribute to an increase in the quantity of the API present at the site of action. Higher drug levels at the active site should particularly increase the effectiveness of a drug with a narrow therapeutic index and reduce the incidence of the resistance that may otherwise arise if the sub-therapeutic levels of the API are in contact with the site of interest. Two approaches were followed in this study. First, the radioactive tracer molecule 99mTechnetium methylene diphosphonate (99mTc MDP) was used. Intravenously injected 99mTc MDP is an extremely effective bone-seeking radiopharmaceutical used in the diagnosis of bone disorders such as bone metastases in patients. However, if entrapped inside a Pheroid vesicle, it will locate to that site, usually an organ, where the Pheroid vesicles may tend to accumulate. Experiments conducted with 99mTc MDP alone or with Pheroid will therefore establish how efficiently Pheroid vesicles localize and will also indicate the preferred site of localization inside a body. The process would involve the oral administration of 99mTc MDP either alone or with Pheroid, involving an animal model. It would also involve tracking localization to particular organs, blood or other sites. The second approach requires the use of chloroquine (CQ) labeled with carbon-14 (14C-CQ,) to compare absorption of the drug both with and without the Pheroid system. The intention was to compare oral absorption and bio-distribution of 14C-CQ administered either alone or entrapped in the Pheroid system. It was also possible to establish whether the Pheroid affects the biological half-lives of the CQ and residence times of CQ in the different organs of the body. Absorption of free 99mTc MDP (orally adminsistered) through the intestinal tract is negligible but it was anticipated that increased absorption will be observed when 99mTc MDP was entrapped in the Pheroid system. In the 99mTc MDP study, different routes of administration of 99mTc MDP, as well as 99mTc MDP entrapped and not entrapped in the Pheroid system, were investigated. The Sprague Dawley rat was used as animal model. Rats were divided into three groups of four rats each for the first part of the study. In the first group, only 99mTc MDP was injected intravenously in order to establish natural distribution of the 99mTc MDP. For the second group, 99mTc MDP was administered orally in order to establish whether there was any absorption through the intestinal tract. In the third group, the 99mTc MDP was entrapped in Pheroid vesicles and this formulation was administered orally in order to establish whether the Pheroid system enhanced oral absorption. The animals were sacrificed four hours after administration and organs were harvested and were counted for radioactivity to determine the percentage of injected/administrated dose in each organ. After oral administration, the Pheroid system was found to have facilitated absorption of 99mTc MDP through the intestinal tract into the blood. 99mTc MDP concentrations in the femur, although lower, were still comparable with that observed after intravenous administration of 99mTc MDP in the absence of Pheroid. Thus, overall, excellent absorption of the Pheroid entrapped 99mTc MDP through the intestinal tract was seen in contrast to little or zero absorption of the compound in the reference formulations. The half-life of the radio-labelled compound in the blood was prolonged after oral administration owing to the Pheroid. To investigate the bio-distribution of radioactive chloroquine (14C-CQ) Sprague Dawley rats were divided into two groups of four rats each. In the first group, 14C-CQ in deionised (DI) water was administered orally, and in the second group 14C-CQ entrapped in Pheroid vesicles was administered, also orally. The animals were sacrificed one, two and four hours after administration and subjected to comprehensive macroscopic inspection. All the organs were harvested and radioactivity was determined with liquid scintillation after applicable sample preparation. The Pheroid system produced much higher organ and blood concentrations of 14C-CQ and enhanced residence times within the organs and blood in comparison with that of 14C-CQ administered alone. Commercial applications of these results are possible, as a number of radiopharmaceutical products can presently be administered only intravenously. The added potential of these new Pheroid formulations could be of significance in the treatment of malaria, as chloroquine is inexpensive and widely available. Another point of interest is that the use of these formulations may enable micromolar drug concentrations to be achieved using drug dosage regimes that usually produce only nanomolar levels. However, safety aspects would have to be carefully monitored. / PhD (Pharmaceutics), North-West University, Potchefstroom Campus, 2015

Previous studies have shown that the formulation of an active pharmaceutical ingredient (API) entrapped in the Pheroid® (Pheroid for simplification) delivery system enhances absorption of the API, suppresses its metabolism, and may contribute to an increase in the quantity of the API present at the site of action. Higher drug levels at the active site should particularly increase the effectiveness of a drug with a narrow therapeutic index and reduce the incidence of the resistance that may otherwise arise if the sub-therapeutic levels of the API are in contact with the site of interest. Two approaches were followed in this study. First, the radioactive tracer molecule 99mTechnetium methylene diphosphonate (99mTc MDP) was used. Intravenously injected 99mTc MDP is an extremely effective bone-seeking radiopharmaceutical used in the diagnosis of bone disorders such as bone metastases in patients. However, if entrapped inside a Pheroid vesicle, it will locate to that site, usually an organ, where the Pheroid vesicles may tend to accumulate. Experiments conducted with 99mTc MDP alone or with Pheroid will therefore establish how efficiently Pheroid vesicles localize and will also indicate the preferred site of localization inside a body. The process would involve the oral administration of 99mTc MDP either alone or with Pheroid, involving an animal model. It would also involve tracking localization to particular organs, blood or other sites. The second approach requires the use of chloroquine (CQ) labeled with carbon-14 (14C-CQ,) to compare absorption of the drug both with and without the Pheroid system. The intention was to compare oral absorption and bio-distribution of 14C-CQ administered either alone or entrapped in the Pheroid system. It was also possible to establish whether the Pheroid affects the biological half-lives of the CQ and residence times of CQ in the different organs of the body. Absorption of free 99mTc MDP (orally adminsistered) through the intestinal tract is negligible but it was anticipated that increased absorption will be observed when 99mTc MDP was entrapped in the Pheroid system. In the 99mTc MDP study, different routes of administration of 99mTc MDP, as well as 99mTc MDP entrapped and not entrapped in the Pheroid system, were investigated. The Sprague Dawley rat was used as animal model. Rats were divided into three groups of four rats each for the first part of the study. In the first group, only 99mTc MDP was injected intravenously in order to establish natural distribution of the 99mTc MDP. For the second group, 99mTc MDP was administered orally in order to establish whether there was any absorption through the intestinal tract. In the third group, the 99mTc MDP was entrapped in Pheroid vesicles and this formulation was administered orally in order to establish whether the Pheroid system enhanced oral absorption. The animals were sacrificed four hours after administration and organs were harvested and were counted for radioactivity to determine the percentage of injected/administrated dose in each organ. After oral administration, the Pheroid system was found to have facilitated absorption of 99mTc MDP through the intestinal tract into the blood. 99mTc MDP concentrations in the femur, although lower, were still comparable with that observed after intravenous administration of 99mTc MDP in the absence of Pheroid. Thus, overall, excellent absorption of the Pheroid entrapped 99mTc MDP through the intestinal tract was seen in contrast to little or zero absorption of the compound in the reference formulations. The half-life of the radio-labelled compound in the blood was prolonged after oral administration owing to the Pheroid. To investigate the bio-distribution of radioactive chloroquine (14C-CQ) Sprague Dawley rats were divided into two groups of four rats each. In the first group, 14C-CQ in deionised (DI) water was administered orally, and in the second group 14C-CQ entrapped in Pheroid vesicles was administered, also orally. The animals were sacrificed one, two and four hours after administration and subjected to comprehensive macroscopic inspection. All the organs were harvested and radioactivity was determined with liquid scintillation after applicable sample preparation. The Pheroid system produced much higher organ and blood concentrations of 14C-CQ and enhanced residence times within the organs and blood in comparison with that of 14C-CQ administered alone. Commercial applications of these results are possible, as a number of radiopharmaceutical products can presently be administered only intravenously. The added potential of these new Pheroid formulations could be of significance in the treatment of malaria, as chloroquine is inexpensive and widely available. Another point of interest is that the use of these formulations may enable micromolar drug concentrations to be achieved using drug dosage regimes that usually produce only nanomolar levels. However, safety aspects would have to be carefully monitored. / PhD (Pharmaceutics), North-West University, Potchefstroom Campus, 2015

<p>Acetolactate synthase (ALS) and acetohydroxyacid synthase (AHAS) are two thiamin diphosphate (ThDP)-dependent enzymes that catalyze the formation of acetolactate from two molecules of pyruvate. In addition to acetolactate, AHAS can catalyze the formation of acetohydroxybutyrate from pyruvate and α-ketobutyrate. When formed by AHAS, these compounds are important precursors to the essential amino acids valine and isoleucine. Conversely, ALS forms acetolactate as a precursor to 2,3‑butanediol, a product formed in an alternative pathway to mixed acid fermentation.</p> <p>While these enzymes catalyze the same reaction, they have been found to be quite different. Such differences include: biological function, pH optimum, cofactor requirements, reaction kinetics and quaternary structure. Importantly, AHAS has been identified as the target of the widely-used sulfonylurea and imidazolinone herbicides, which has led to many structural and kinetic studies on AHAS enzymes from plants, bacteria, and fungi. ALS, on the other hand, has only been identified in bacteria, and has largely not seen such extensive characterization. Finally, although some bacteria contain both enzymes, they have never been studied in detail from the same organism. </p> <p>Here, the ALS and AHAS enzymes from <i>Klebsiella pneumoniae</i> were studied using steady-state kinetic analyses, X-ray crystallography, site-directed and site‑saturation mutagenesis, and cell growth complementation assays to i) compare the kinetic parameters of each enzyme, ii) compare the active sites to probe their differences in substrate profile and iii) test the ability of ALS to function in place of AHAS <i>in vivo</i>.</p>