Dissertations / Theses on the topic 'NADH molecules'

Biosensors have proven to be a powerful tool for detecting diverse targets, such as proteins, DNA, and small molecules representing disease biomarkers, toxins, drugs and their metabolites, environmental pollutants, agrichemicals, and antibiotics with high sensitivity and specificity. The major objective of the research described in this dissertation was to develop low cost, low sample volume, highly sensitive and specific AuNP-based colorimetric sensor platforms for the detection of DNA and small molecules. With this in mind, we propose an instrument-free approach in chapter three for the detection of NADH with a sensor constructed on a paper substrate, based on the target-induced inhibition of AuNP dissolution. The successful detection of this important molecule opens the door to numerous possibilities for dehydrogenase characterization, because NAD+/NADH are essential cofactors for more than 300 dehydrogenase enzymes. To further increase the sensitivity of our hybridization-based assay for DNA detection, we developed an enzyme-assisted target recycling (EATR) strategy in chapter four and have applied such an EATR-based colorimetric assay to detect single-nucleotide mismatches in a target DNA with DNA-functionalized AuNPs. This assay is based on the principle that nuclease enzymes recognize probe–target complexes, cleaving only the probe strand. This results in target release, enabling subsequent binding to and cleavage of another probe molecule. When the probe is conjugated onto AuNPs, complete cleavage from the AuNP surface produces a detectable signal in high ionic strength environments as the nanoparticles undergo aggregation. With such enzyme-assisted amplification, target detection can occur with a very low nM detection limit within 15 minutes. The extent of DNA loading on the AuNP surface plays an important role in the efficiency of DNA hybridization and aptamer-target assembly. Many studies have shown that high surface-coverage is associated with steric hindrance, electrostatic repulsive interactions and elevated surface salt concentration, whereas low surface-coverage can result in nonspecific binding of oligonucleotides to the particle surface. In chapter five, we investigated DNA surface coverage effects, and apply this optimization in conjunction with a highly-specific aptamer to develop a sensitive colorimetric sensor for rapid cocaine detection based on the inhibition of nuclease enzyme activity.

NADH and NADPH are ubiquitous biological reducing agents essential for both respiration and biosynthesis. The discovery that increased pentose-phosphate pathway activity in cervical cancer cells leads to increased levels of NAD(P)H, emphasises the need for a sensitive detection system as an indication of cellular viability and vitality. The remit of this project was to design and synthesise a novel molecular sensor system whose emissive properties are "switched on" upon reduction by NAD(P)H. Research using the reducible, non-fluorescent dye, resazurin, has shown that, in the presence of a non-enzymic electron transfer agent phenazinium methosulphate (PMS)-NADH can effect reduction to the highly fluorescent dye resorufin. Mechanistic studies have shown that the reduction proceeds via a two-electron hydride transfer to the heterocyclic mediator, followed by a one electron transfer to the dye and disproportionation to furnish the final fluorescent product. It has been shown that direct reduction by NADH does not occur and that the reaction depends upon there being an electron transfer agent present. A new type of reagent for the detection of NAD(P)H has been synthesised, comprising a reducible heterocycle and a masked fluorophore. It has been shown that reduction of the precursor conjugate by NADH results in the release of a detectable fluorescent moiety methylumbelliferone. The synthesis of an analogous conjugate probe containing a known hindered dioxetane moiety is described. Prepared using a previously unreported route, the key vinyl ether intermediate is generated via a Wadsworth-Emmons reductive coupling of an alkoxy phosphonate to 2-adamantanone. Reduction by NADH and subsequent cleavage of a conjugate ether link generates an electron rich phenolate substituted dioxetane which is metastable, resulting in emission from the generated excited product. Work towards a dioxetane containing functionalised alkyl group for conjugation to a fluorophore is also outlined.

Biological wastewater treatment relies on the diverse and complex metabolic activities of bacteria to remove pollutants. Its success depends on the metabolic efficiency of the bacteria. Activated sludge models use parameters that attempt to depict bacterial growth and metabolic processes. However, current methods do not separate metabolic activity from growth and maintenance. As a result, activated sludge processes are misinterpreted or over-simplified. Alternative methods for gauging bacterial activity have been proposed and include the measurements of cellular derived compounds that relate specifically to energy cycling and include Nicotinamide Adenine Dinucleotide [NADH]. To date, NADH has been largely measured within activated sludge using commercial online fluorimeters with in situ probes. However, this current method provides a measure of the 'bulk' (raw) fluorescence within the system, resulting in difficulties when interpreting fluorescence data and poor sensitivity for detecting changes in intracellular [NADH]. This study has developed a more reliable method for estimating intracellular [NADH] and thus metabolic activity within activated sludge systems. Separating extracellular from intracellular [NADH] in samples was crucial because NADH was released and accumulates in the extracellular environment at a concentration of 200 ~M immediately following bacterial death or lysis. This concentration did not decline overtime. This not only caused high background fluorescence but also reduced the sensitivity of detection for changes in intracellular [NADH]. In particular, considerably higher [NADH] values to those from the extracellular suspensions were obtained following extraction of the intracellular material, suggesting that the cell membranes were not being penetrated by the excitable light source. Of the extraction procedures examined, filtration followed by extraction of the intracellular material with a hot Tris buffer was the most efficient and was recommended for accurate estimates of intracellular [NADH] in situ. In addition, standards were used to quantify NADH (moles per cell and/or unit volume) from unknown samples. The limits of detection were found to be 1.058 - 353 uM, whereas concentrations above 353 jAM self-quenched. Sample concentrations were always within these limits of detection. Hence, the sensitivity, reliability and experimental application of the original method was improved upon and able to be used for the direct measurement of microbial metabolic activity, something that has not been demonstrated before now. This study found that bacteria have between 106~ I 08 NADH molecules per cell depending on their metabolic state. A highly metabolically active bacterial cell had between 1O6~ tO7 NADH molecules, while a less active bacterial cell had between to7 -to8 NADH molecules. These measurements of metabolic activity were simultaneously monitored alongside other measures of bacterial growth, such as the incorporation of radiolabelled thymidine into DNA as a direct measure of DNA replication (new cell synthesis), the incorporation of radiolabelled leucine into protein as a direct measure of protein synthesis, oxygen uptake rates (OUR) as a direct measure of respiration, ATP as a measure of potential energy and dissolved organic carbon (DOC) as a measure of substrate assimilation. As OUR deceased, bacterial growth (using both the thymidine and leucine assays), specific [NADH] and specific [ATP] increased. High OUR and substrate oxidation rates simultaneous with low specific [NADH] indicated high rates of electron transport and thus efficient metabolic activity. Also, low OUR and substrate oxidation rates simultaneous with high specific [NADHI indicated inefficient rates of electron transport, therefore inhibiting oxidative phosphorylation (ATP production). A lack of oxygen as the terminal electron acceptor did not efficiently reoxidise NADH to NAD and resulted in an accumulation of NADH within the cell. Thus, a measure of low specific [NADHI was linked to the efficient rate of reoxidation of NADH to NAD* and reflects high metabolic efficiency. DNA and protein syntheses were coupled following substrate enrichment (glucose or acetate), indicating that bacteria were in balanced growth. However, DNA and protein syntheses became uncoupled once substrate was depleted, indicating unbalanced growth. An average Leu:TdR ratio of 7.4 was determined for activated sludge and was comparable to values published from marine systems. This ratio increased during log growth phase and decreased during stationary growth phases. Specific growth rates determined using the [3HITdR and [3H]Leu assay yielded values ranging from 2 - 10.5 d' and from 2.5 - 6 d1, respectively and were comparable to published values. Changes in OUR, NADH, ATE', DNA replication and protein synthesis were statistically ordinated using multidimensional scaling, and changes (in magnitude and direction) in bacterial metabolic activity were observed. Such methods enable the tracing of where bacteria divert their energies, such as to growth or maintenance and thus provide a greater understanding of bacterial behaviour in activated sludge. While studying anoxic and anaerobic conditions were beyond the scope of this work, the use of such methods to monitor bacterial metabolic activity under such conditions is warranted.

Biological wastewater treatment relies on the diverse and complex metabolic activities of bacteria to remove pollutants. Its success depends on the metabolic efficiency of the bacteria. Activated sludge models use parameters that attempt to depict bacterial growth and metabolic processes. However, current methods do not separate metabolic activity from growth and maintenance. As a result, activated sludge processes are misinterpreted or over-simplified. Alternative methods for gauging bacterial activity have been proposed and include the measurements of cellular derived compounds that relate specifically to energy cycling and include Nicotinamide Adenine Dinucleotide [NADH]. To date, NADH has been largely measured within activated sludge using commercial online fluorimeters with in situ probes. However, this current method provides a measure of the 'bulk' (raw) fluorescence within the system, resulting in difficulties when interpreting fluorescence data and poor sensitivity for detecting changes in intracellular [NADH]. This study has developed a more reliable method for estimating intracellular [NADH] and thus metabolic activity within activated sludge systems. Separating extracellular from intracellular [NADH] in samples was crucial because NADH was released and accumulates in the extracellular environment at a concentration of 200 ~M immediately following bacterial death or lysis. This concentration did not decline overtime. This not only caused high background fluorescence but also reduced the sensitivity of detection for changes in intracellular [NADH]. In particular, considerably higher [NADH] values to those from the extracellular suspensions were obtained following extraction of the intracellular material, suggesting that the cell membranes were not being penetrated by the excitable light source. Of the extraction procedures examined, filtration followed by extraction of the intracellular material with a hot Tris buffer was the most efficient and was recommended for accurate estimates of intracellular [NADH] in situ. In addition, standards were used to quantify NADH (moles per cell and/or unit volume) from unknown samples. The limits of detection were found to be 1.058 - 353 uM, whereas concentrations above 353 jAM self-quenched. Sample concentrations were always within these limits of detection. Hence, the sensitivity, reliability and experimental application of the original method was improved upon and able to be used for the direct measurement of microbial metabolic activity, something that has not been demonstrated before now. This study found that bacteria have between 106~ I 08 NADH molecules per cell depending on their metabolic state. A highly metabolically active bacterial cell had between 1O6~ tO7 NADH molecules, while a less active bacterial cell had between to7 -to8 NADH molecules. These measurements of metabolic activity were simultaneously monitored alongside other measures of bacterial growth, such as the incorporation of radiolabelled thymidine into DNA as a direct measure of DNA replication (new cell synthesis), the incorporation of radiolabelled leucine into protein as a direct measure of protein synthesis, oxygen uptake rates (OUR) as a direct measure of respiration, ATP as a measure of potential energy and dissolved organic carbon (DOC) as a measure of substrate assimilation. As OUR deceased, bacterial growth (using both the thymidine and leucine assays), specific [NADH] and specific [ATP] increased. High OUR and substrate oxidation rates simultaneous with low specific [NADH] indicated high rates of electron transport and thus efficient metabolic activity. Also, low OUR and substrate oxidation rates simultaneous with high specific [NADHI indicated inefficient rates of electron transport, therefore inhibiting oxidative phosphorylation (ATP production). A lack of oxygen as the terminal electron acceptor did not efficiently reoxidise NADH to NAD and resulted in an accumulation of NADH within the cell. Thus, a measure of low specific [NADHI was linked to the efficient rate of reoxidation of NADH to NAD* and reflects high metabolic efficiency. DNA and protein syntheses were coupled following substrate enrichment (glucose or acetate), indicating that bacteria were in balanced growth. However, DNA and protein syntheses became uncoupled once substrate was depleted, indicating unbalanced growth. An average Leu:TdR ratio of 7.4 was determined for activated sludge and was comparable to values published from marine systems. This ratio increased during log growth phase and decreased during stationary growth phases. Specific growth rates determined using the [3HITdR and [3H]Leu assay yielded values ranging from 2 - 10.5 d' and from 2.5 - 6 d1, respectively and were comparable to published values. Changes in OUR, NADH, ATE', DNA replication and protein synthesis were statistically ordinated using multidimensional scaling, and changes (in magnitude and direction) in bacterial metabolic activity were observed. Such methods enable the tracing of where bacteria divert their energies, such as to growth or maintenance and thus provide a greater understanding of bacterial behaviour in activated sludge. While studying anoxic and anaerobic conditions were beyond the scope of this work, the use of such methods to monitor bacterial metabolic activity under such conditions is warranted.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environmental Engineering
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Heterologous expression systems such as COS-7 cells have demonstrated the profound effects of KCNAB1-3 or Kvβ1-3 proteins on voltage gated potassium channels (Kv) channels. Indeed, in the presence of these β-subunits transiently expressed Kv channels are often modulated in multiple ways. Kv channel membrane expression is often increased in the presence of β-subunits. In addition, non-inactivating Kv currents suddenly become fast-inactivating and fast-inactivating channels become even faster. While much research has demonstrated the profound effects the β-subunits in particular the Kvβ1 subunit have on transiently expressed Kv currents little to date is known of the physiological role it may play. One study demonstrated that by “knocking out” Kvβ1 cardiomyocyte current changes were noted including a decrease in the Ito,f current. While this novel finding demonstrated a key cardiac physiological role of the Kvβ1 subunit it left many unanswered questions as to determine the cardiovascular regulation the Kvβ1 subunit provides. Indeed, cardiac arrhythmias and other electrical abnormalities within the heart such as long QT present patients with many unfortunate unknowns. Many of these incidences occur often abruptly with cardiac electrical abnormalities. Genetic research has begun to shine light on key cardiovascular genes in particular those coding for ion channels and auxiliary subunits or β-subunits. Kv channels and their β-subunits have gained particular notoriety in their key responsibility in restoring the resting membrane potential known as the repolarization phase. Indeed genetic manipulation and physiological examination of Kv channels and recently their β-subunits has demonstrated profound physiological results including prolonged QT durations within mice altered functional activity during physiological cycles such as estrus. While initial findings of Kvβ1 have demonstrated profound cellular and cardiomyocyte current alterations much still remains unknown. Therefore, this work hypothesizes that the Kvβ1 subunit provides a profound cardiovascular role in regulation and redox sensing at the physiological and pathophysiological level in both males and females. This work identifies a sex-based difference in cardiovascular regulation by Kvβ1 as well as demonstrated a profound redox sensing ability during altered metabolic states seen in pathophysiological conditions.

Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro
Evidências têm mostrado que as espécies reativas de oxigênio (ROS) geradas pela NAD(P)H oxidase são importantes moduladores de diversas funções celulares como migração, crescimento, proliferação e sobrevivência. Estudos recentes demonstraram o envolvimento da atividade da NAD(P)H oxidase no crescimento e sobrevivência de células de melanoma. Neste trabalho, investigamos o efeito da inibição da NAD(P)H oxidase por difenileneiodônio (DPI) sobre o crescimento das células de melanoma humano MV3 e observamos que este composto reduziu o crescimento destas células em aproximadamente 50%. A inibição da NAD(P)H oxidase induziu mudanças no formato celular, com arredondamento, diminuição do espraiamento e descolamento celular. Esta redução foi acompanhada por um rearranjo do citoesqueleto de actina, diminuição da fosforilação no resíduo Tyr397 da quinase de adesão focal (FAK) e redução na associação de FAK com actina e com a tirosina quinase c-Src. Isto indica que a inibição da geração de ROS está modulando negativamente vias de sinalização ativadas por integrinas, o que freqüentemente conduz a um tipo particular de morte celular conhecida por anoikis. Comprovando a ocorrência deste fenômeno, observamos que a inibição da atividade da NAD(P)H oxidase aumentou a apoptose das células de melanoma e induziu a ativação da caspase-3. Nossos resultados mostram ainda que a inibição da viabilidade celular por DPI foi revertida com o pré-tratamento das células MV3 com um inibidor de tirosina fosfatases (ortovanadato de sódio). Em resumo, este estudo mostra que a geração de ROS por NAD(P)H oxidase está envolvida nos mecanismos de sobrevivência em células de melanoma, uma vez que afetam as vias de sinalização dependentes de FAK-Src, através da inibição da atividade de proteína tirosina fosfatases.
NAD(P)H oxidase-derived reactive oxygen species (ROS) have emerged as critical mediators of several cell functions as diverse as migration, growth, proliferation and survival. Recent evidence has show that NAD(P)H oxidase activity is essential to melanoma proliferation and survival. We reported that NAD(P)H oxidase inhibitor diphenyleneiodonium (DPI) inhibited melanoma growth. NAD(P)H oxidase inhibition induced changes in cell shape with cell spreading decrease, rounding up and detachment. These phenomena were accompanied by rearrangement of actin network and a decrease in both focal adhesion (FAK) phosphorylation in Tyr397 residue and in FAK association to actin and c-Src, indicating that inhibition of ROS generation would down- modulate integrin-mediated signaling, what often results in a particular type of apoptotic cell death, known as anoikis. We observed that NAD(P)H oxidase inhibitor induced apoptosis in melanoma cells with activation of caspase-3. We results show that the effects promoted by NAD(P)H oxidase inhibition on melanoma growth were completely abolished by the pre-treatment of MV3 cells with the protein tyrosine phosphatases inhibitor sodium orthovanadate. In conclusion, our results strongly suggest that ROS generated by NAD(P)H oxidase complex transmit cell survival signals in melanoma cells through the FAK-Src pathway, probably inhibiting protein tyrosine phosphatases.

Over the past few decades, RNA has emerged as much more than just an intermediary in biology’s central dogma. RNA is now known to play a variety of catalytic, regulatory and defensive roles in living systems as demonstrated through the discoveries of ribozymes, riboswitches, microRNAs, small interfering RNAs, Piwi-interacting RNAs, small nuclear RNAs, clusters of regularly interspaced short palindromic repeat RNAs and long non-coding RNAs. In contrast to the functional diversity of RNA, the chemical diversity has remained primarily limited to canonical polyribonucleotides, the 5’ cap on mRNAs in eukaryotes, modified nucleotides and 3’-aminoacylated tRNAs. This disparity coupled with the powerful functional properties of small molecule-nucleic acid conjugates led us to speculate that novel small molecule-RNA conjugates existed in modern cells, either as evolutionary fossils or as RNAs whose functions are enabled by the small molecule moieties. We developed and applied a nuclease-based screen coupled with high-resolution liquid chromatography/mass spectrometry analysis to detect novel small molecule-RNA conjugates, broadly and sensitively. We discovered NAD-linked RNA in two types of bacteria and further characterized the small molecule and RNA in Escherichia coli. The NAD modification is found on the 5’ end of RNAs between 30 and 120 nucleotides long, and is surprisingly abundant at around 3,000 copies per cell. Subsequent experiments to characterize further NAD-linked RNA have been undertaken, including sequencing the RNAs to which NAD is attached and elucidating the biological functions of the small molecule-RNA conjugate. The development and application of a screen to detect novel nucleotide modifications that is independent of structure or biological context has the potential to increase our understanding of the functional and chemical diversity of RNA. The discovery and biological characterization of NAD-linked RNA can provide new examples of RNA biology and offer insight into the RNA world.

Le polynucléaire neutrophile (PMN), cellule clé de l’immunité innée, est la première cellule à être recrutée sur le site inflammatoire. Après avoir détruit l’agent pathogène, il entre en apoptose puis est éliminé par les macrophages pour éviter le déversement de son contenu lytique, dangereux pour l’environnement. La régulation de la balance survie/apoptose du neutrophile est donc une étape cruciale de la résolution de l’inflammation. Notre laboratoire a mis en évidence la présence du Proliferating Cell Nuclear Antigen (PCNA) dans le neutrophile mature. PCNA est exprimé dans le noyau des cellules proliférantes, où il est impliqué dans la réplication/réparation de l’ADN et dans le contrôle du cycle cellulaire. PCNA est une protéine trimérique conservée au cours de l’évolution dépourvue d’activité enzymatique. En effet, PCNA constitue une “plateforme” qui interagit avec différents partenaires protéiques et orchestre leurs fonctions. De plus, pour assurer sa fonction, PCNA doit être obligatoirement sous forme trimérique. Dans le neutrophile mature, il a été démontré que PCNA avait une localisation exclusivement cytosolique et qu’il contrôlait spécifiquement la survie du neutrophile. La translocation de PCNA du noyau au cytosol a lieu pendant la différenciation granulocytaire. Elle est dépendante d'une séquence d'export nucléaire (NES) accessible et fonctionnelle que lorsque PCNA est monomérique. Le but de ma thèse a été d’étudier la plateforme de PCNA dans le cytosol du neutrophile afin d'identifier les protéines associées à PCNA afin de comprendre sa fonction dans les neutrophiles. Nous avons montré la présence de la forme monomérique et de la forme trimérique de PCNA dans le cytosol du neutrophile mature. Nous avons démontré une activité anti-apoptotique de la forme monomérique dans des cellules PLB985 différenciées en neutrophiles. De plus, nous avons identifié des peptides exposés sur la surface monomérique de PCNA qui sont utilisé comme des compétiteurs pour déplacer les interactions entre PCNA et ses partenaires dans le cytosol des neutrophiles. Ces peptides modulent la survie des neutrophiles. Grâce à des analyses de Spectrométrie de Masse, nous avons identifié des nouveaux partenaires de PCNA dans le cytosol du neutrophile impliqués dans plusieurs voies métaboliques. Cela suggère que PCNA régule la survie du neutrophile en interagissant avec différents protéines cytosoliques. Parmi les partenaires identifiés, nous avons trouvé les sous-unités cytosoliques de la NADPH oxydase, enzyme responsable de la production de formes réactives de l’oxygène, à la base de l’activité microbicide du neutrophile. Nous avons montré en particulier l’interaction entre p47phox et PCNA. Nous avons enfin étudié l’implication fonctionnelle de l’interaction de PCNA avec la NADPH oxydase dans des cellules PLB985 et également dans des neutrophiles humains. L’ensemble des résultats suggère que PCNA cytoplasmique maintient le neutrophile dans un état de repos, et aide l’assemblage de la NADPH oxydase lors de son activation. Le réseau protéique associé à PCNA régule l’activité et la survie du neutrophile en modulant différentes voies de signalisation
Polymorphonuclear neutrophils (PMN), key cells of innate immunity are the first cell recruited to the inflammatory site. After destroying the pathogen, neutrophils undergo apoptosis and are cleared by macrophages to prevent the spillage of their lytic content that is dangerous for the environment. The regulation of the survival/apoptosis balance of neutrophil is a crucial step in the inflammation resolution. Our laboratory has shown the presence of Proliferating Cell Nuclear Antigen (PCNA) in mature neutrophils. PCNA is expressed in the nucleus of proliferating cells, where it is involved in DNA replication/repair and in cell cycle control. PCNA is a trimeric protein conserved during evolution and deprived of enzymatic activity. Indeed, PCNA is a “platform” that interacts with different partner proteins and orchestrates their functions. Furthermore, PCNA must be in trimeric form to play its role. In mature neutrophils, PCNA has an exclusively cytosolic localization where it specifically controls their survival. The PCNA translocation from nucleus to the cytosol happened during the granulocytic differentiation. This nuclear-to-cytosol relocalisation is dependent on a nuclear export sequence (NES), which is accessible and functional when PCNA is monomeric. The aim of my thesis was to study the PCNA platform in the neutrophil cytosol to identify the proteins associated with PCNA in order to understand its function in neutrophils. We have shown the expression of monomeric and trimeric forms of PCNA in the cytosol of mature neutrophils. We have demonstrated the anti-apoptotic activity of the monomeric form in PLB985 cells differentiated in neutrophils. Moreover, we have identified the surface-exposed peptides from the monomeric PCNA which are used as competitors of interactions between PCNA and its partner in the cytosol of neutrophils. These peptides modulate neutrophils survival. Thanks to the analysis of Mass Spectrometry, we have identified new partners of PCNA in the neutrophil cytosol involved in several metabolic pathways. This suggests that PCNA regulates neutrophil survival by interacting with different cytosolic proteins. Among the identified partners, we have found the cytosolic subunits of the NADPH oxidase, the enzyme responsible of the reactive oxygen species production, at the base of the neutrophil microbicidal activity. We have shown especially the interaction between p47phox and PCNA. Finally, we have investigated the functional implication of the interaction of PCNA with the NADPH oxidase in PLB985 cells and also in human neutrophils. Taken altogether, results suggest that the cytosolic PCNA maintains the resting state of neutrophils, and it helps the assembly of the NADPH oxidase when activated. The protein network associated with PCNA regulates the activity and the survival of neutrophil by modulating several pathways

Doctor en ciencias Biomédicas
Physical activity plays a protective role in the development of chronic non-communicable diseases. Molecular adaptations explain the beneficial effects of exercise in diverse tissues such as skeletal muscle, adipose tissue, and heart. One of the multiple signals involved in the benefits of exercise are the oxidation-reduction reactions called redox signaling. Reversible and non-reversible posttranslational modifications of cysteine residues are capable of changing the function, localization, or stability of diverse proteins. In skeletal muscle, reactive oxygen species (ROS) are continuously produced and cleared during resting and contracting conditions. There is substantial evidence indicating that redox signaling plays a role in some of the health-benefits elicited by endurance training, however, the precise mechanism has been long unknown. The aim of the current Ph.D. thesis was therefore to study the involvement of NOX2 and redox signals in the regulation of exercise-stimulated glucose transport and adaptive gene expression in mature skeletal muscle. A combination of pharmacological inhibitors and murine NOX2-deficient models were used to address the necessity of NOX2 for glucose transport and adaptive signals induced by acute exercise. The current Ph.D. thesis demonstrated for the first time that NOX2 is activated during moderateintensity endurance exercise in skeletal muscle and it is a major source of ROS under those conditions. Furthermore, the analyses of genetic mouse models lacking the regulatory NOX2 subunits p47phox and Rac1 revealed striking phenotypic similarities, including severely impaired exercise-stimulated glucose uptake and GLUT4 translocation, indicating that NOX2 is a requirement for this classic acute myocellular adaptation to exercise. Overall, NOX2 is thus a major ROS source regulating adaptive responses to exercise in skeletal muscle.
La actividad física juega un papel protector en el desarrollo de enfermedades crónicas no transmisibles. Las respuestas moleculares explican los efectos beneficiosos del ejercicio en diversos tejidos como el músculo esquelético, el tejido adiposo y el corazón. Una de las múltiples señales involucradas en los beneficios del ejercicio son las reacciones de oxidación-reducción llamadas señalización redox. Las modificaciones postraduccionales reversibles e irreversibles de residuos de cisteína son capaces de cambiar la función, localización o estabilidad de diversas proteínas. En el músculo esquelético, las especies de oxígeno reactivo (ROS) se producen y eliminan continuamente durante las condiciones de reposo y contracción. Existe evidencia sustancial que indica que la señalización redox juega un papel en algunos de los beneficios para la salud provocados por el entrenamiento de resistencia, sin embargo, el mecanismo preciso ha sido desconocido durante mucho tiempo. El objetivo de la presente la tesis fue estudiar la participación de NOX2 en la regulación del transporte de glucosa durante el ejercicio y la expresión de genes adaptativos en el músculo esquelético adulto. Se utilizó una combinación de inhibidores farmacológicos y modelos deficientes en NOX2 ratón para abordar la necesidad de NOX2 para el transporte de glucosa y las señales adaptativas inducidas por el ejercicio agudo. Esta tesis demostró por primera vez que el NOX2 se activa durante el ejercicio de resistencia de intensidad moderada en el músculo esquelético y es una fuente importante de ROS en esa condición. Además, los análisis de modelos de ratones genéticos que carecen de las subunidades reguladoras NOX2 p47phox y Rac1 revelaron sorprendentes similitudes fenotípicas, incluida la captación de glucosa estimulada por el ejercicio y la translocación de GLUT4, lo que indica que NOX2 necesaria para esta respuesta fisiológica durante el ejercicio. En resumen, NOX2 es, por lo tanto, una importante fuente de ROS que regula las respuestas de adaptación al ejercicio en el músculo esquelético.
22/03/2020

A doença granulomatosa crônica é uma imunodeficiência primária dos fagócitos causada por mutações no sistema NADPH oxidase resultando em burst oxidativo ausente ou reduzido. Nosso objetivo foi realizar uma análise genética molecular do complexo NADPH oxidase em pacientes com diagnóstico clínico de DGC. Cinqüenta e quatro pacientes com diagnóstico clínico sugestivo da DGC foram incluídos em nosso estudo. As populações de neutrófilos e monócitos foram avaliadas pela capacidade de produzir peróxido de hidrogênio por meio do teste de DHR. Dezoito pacientes apresentaram defeito no burst oxidativo, enquanto trinta e oito apresentaram produção de peróxido normal. O DNA genômico dos dezoito pacientes com burst oxidativo diminuído foi extraído, os genes da cadeia beta polipeptídica do complexo citocromo b e o factor citoplasmático de neutrófilos, foram sequenciados. Sete pacientes apresentaram diferentes mutações, tanto no gene CYBB como no NCF1. Concluímos que a combinação do teste de DHR e o sequenciamento direto são métodos eficazes para o diagnóstico genético da DGC.
Chronic granulomatous disease is a primary immunodeficiency caused by mutations in the phagocyte NADPH oxidase system resulting in absent or reduced oxidative burst. Our goal was to perform a molecular genetic analysis of complex NADPH oxidase in patients with clinical diagnosis of CGD. Fifty-four patients with a clinical diagnosis of CGD were included in our study. The populations of neutrophils and monocytes were evaluated for the ability to produce hydrogen peroxide through the DHR test. Eighteen patients had a defect in the oxidative burst, while thirty-eight had normal peroxide production. Genomic DNA of the eighteen patients with decreased oxidative burst was extracted, the genes the chain complex cytochrome beta polypeptide and the neutrophil cytoplasmic factor, were sequenced. Seven patients had different mutations, both in the CYBB gene as in NCF1. We conclude that the combination of direct sequencing and DHR test methods are effective for the genetic diagnosis of CGD.

La Quinolinate synthase (NadA) catalyse la condensation de l'iminoaspartate et de la dihydroxyacétone phosphate aboutissant à la formation d'acide quinolinique, un intermédiaire central dans la biosynthèse du nicotinamide adénine dinucléotide (NAD). Cette étude a permis de montrer que toutes les quinolinate synthases possèdent un centre [4Fe-4S] essentiel à l'activité et que seulement 3 résidus cystéines coordinent le centre métallique, les cystéines Cys113, Cys200 et Cys297 chez E. coli. Les propriétés spectroscopiques et biochimiques du centre [4Fe-4S] nous ont conduit à proposer que le centre fer-soufre joue un rôle de type aconitase/déshydratase dans la catalyse enzymatique. Deux autres cystéines impliquées dans la formation d'un pont disulfure, sont également essentielles à l'activité quinolinate synthase (Cys291 et Cys294 chez E. coli) en jouant probablement un rôle régulateur. Nous rapportons également une nouvelle hypothèse de mécanisme pour la formation de l'acide quinolinique, incluant l'isomérisation du glycéraldéhyde 3-phosphate en DHAP. Enfin, nous proposons NadA comme une cible potentielle d'agents antibactériens. Sur les différentes molécules testées in vitro, l'acide phosphoglycolohydroxamique (PGH) s'est avérée actif sur la quinolinate synthase d'E. coli et de M. tuberculosis, en agissant comme un inhibiteur compétitif du DHAP.

Cells utilize various signal transduction networks to regulate metabolism. Nevertheless, a quantitative understanding of the relationship between growth factor signaling and metabolic state at the single cell level has been lacking. The signal transduction and metabolic states could vary widely among individual cells. However, such cell-to-cell variation might be masked by the bulk measurements obtained from conventional biochemical methods. To assess the spatiotemporal dynamics of metabolism in individual intact cells, we developed genetically encoded biosensors based on fluorescent proteins. As a key redox cofactor in metabolism, NADH has been implicated in the Warburg effect, the abnormal metabolism of glucose that is a hallmark of cancer cells. To date, however, sensitive and specific detection of NADH in the cytosol of individual live cells has been difficult. We engineered a fluorescent biosensor of NADH by combining a circularly permuted green fluorescent protein variant with a bacterial NADH-binding protein Rex. The optimized biosensor Peredox reports cytosolic \(NADH:NAD^+\) ratios in individual live cells and can be calibrated with exogenous lactate and pyruvate. Notably pH resistant, this biosensor can be used in several cultured and primary cell types and in a high-content imaging format. We then examined the single cell dynamics of glycolysis and energy-sensing signaling pathways using Peredox and other fluorescent biosensors: AMPKAR, a sensor of the AMPK activity; and FOXO3-FP, a fluorescently-tagged protein domain from Forkhead transcription factor FOXO3 to report on the PI3K/Akt pathway activity. With perturbation to growth factor signaling, we observed a transient response in the cytosolic \(NADH:NAD^+\) redox state. In contrast, with partial inhibition of glycolysis by iodoacetate, individual cells varied substantially in their responses, and cytosolic \(NADH:NAD^+\) ratios oscillated between high and low states with a regular, approximately half-hour period, persisting for hours. These glycolytic NADH oscillations appeared to be cell-autonomous and coincided with the activation of the PI3K/Akt pathway but not the AMPK pathway. These results suggest a dynamic coupling between growth factor signaling and metabolic parameters. Overall, this thesis presents novel optical tools to assess metabolic dynamics – and to unravel the elaborate and complex integration of glucose metabolism and signaling pathways at the single cell level.

A principal função da glândula tireoide é a produção dos hormônios T3 e T4, que promovem a regulação do consumo energético no organismo. O hipotireoidismo congênito (HC) é um distúrbio metabólico sistêmico, onde a produção de T3 e T4 no período neonatal é insuficiente. O HC por disormonogênese é uma doença causada por erros inatos na síntese de T3 e T4, com herança autossômica recessiva. Já foram descritas mutações nos genes NIS, SLC26A4, DUOX2, DUOXA2, TPO, TG e DEHAL-1. O defeito na organificação do iodeto (DOI) é o mais comum na disormonogênese, sendo a falha mais frequente na TPO, seguida pelas proteínas DUOX2 e DUOXA2. A TPO é responsável pela oxidação do iodeto, pela iodação da tireoglobulina e pelo acoplamento das tirosinas iodinizadas. Já foram descritas 70 mutações ao longo de todo o gene TPO. Por ser uma heme peroxidase, a TPO requer H2O2 para sua função. O principal núcleo catalítico gerador de H2O2 na tireoide é o complexo DUOX2/DUOXA2. Foram descritas 25 mutações no gene DUOX2 e uma única mutação no gene DUOXA2. Em estudo anterior, avaliamos pacientes com HC após os 3 anos de idade para estabelecimento do diagnóstico etiológico, através de dosagem de TG sérica, ultrassonografia, captação e mapeamento da tireoide com 131I. Sete pacientes apresentaram DOI. Nestes pacientes avaliamos o gene TPO e identificamos diversos SNPs já descritos na literatura. Um paciente apresentou a mutação p.Q660E em heterozigose, outro paciente o SNP p.R584Q em homozigose, e um terceiro paciente as alterações p.Q660E e p.584Q em heterozigose composta. Os objetivos deste estudo foram pesquisar mutações dos genes DUOX2 e DUOXA2 nos pacientes com DOI e realizar o estudo funcional da alteração p.R584Q na TPO. Para o estudo molecular, extraímos o DNA de leucócitos periféricos dos pacientes e seus familiares, seguido de amplificação por PCR, e sequenciamento automático, e os resultados comparados com as sequencias normais de cada gene (GenBank). Na análise funcional da alteração p.R584Q na TPO, células HeLa foram transfectadas com plasmídios pcDNA contendo o gene da TPO normal e alterado, e a atividade das proteínas produzidas pelas células foi avaliada pelo sistema AmplexRed. Análises in silico foram realizadas com os programas de bioanálise PolyPhen, MutationTaster, SIFT e PSIPRED. Ao final do estudo molecular, no gene DUOX2, identificamos 20 SNPs previamente descritos, incluindo o SNP funcional p.H678R (rs57659670), presente em heterozigose em 3 pacientes. Também identificamos a nova substituição p.A1087V em heterozigose em um paciente. De acordo com dados dos programas de bioanálise, a alteração p.A1087V é prejudicial e o SNP p.H678R é tolerável. No gene DUOXA2 identificamos 5 polimorfismos previamente descritos e nenhuma mutação. No estudo funcional, verificamos uma diminuição significativa da atividade da TPO portadora da alteração p.R584Q em comparação à proteína normal (5% de atividade residual; p=0,0193). De acordo com os dados dos programas de bioanálise, a alteração p.R584Q é prejudicial. Três pacientes não apresentaram alterações nas regiões estudadas dos genes TPO, DUOX2 e DUOXA2. As revisões dos dados clínicos e laboratoriais sugerem a presença de outras proteínas alteradas, como TG, Pendrina ou receptor do TSH. Um paciente apresentou a nova alteração p.A1087V na DUOX2 em heterozigose e nenhuma outra alteração nas regiões estudadas dos genes avaliados. Cogitamos a presença de alterações em regiões não avaliadas ou ainda a expressão monoalélica de DUOX2. O SNP funcional p.H678R na DUOX2 foi identificado em três pacientes com alterações na TPO: um com a alteração p.R584Q em homozigose, outro com a p.R584Q e a mutação p.Q660E em heterozigose composta. Estes dois pacientes apresentam os dois alelos da TPO alterados, justificando o DOI. O terceiro caso apresentou apenas a mutação p.Q660E em heterozigose, podendo apresentar alterações em regiões não avaliadas ou ainda a expressão monoalélica da TPO. Concluímos que definimos o diagnóstico molecular de 4 dos nossos pacientes, que apresentaram importantes alterações nos genes avaliados, e ressaltamos que a alteração p.R584Q na TPO provoca perda da atividade, causando DOI
The main role of the thyroid gland is to produce T3 and T4, which promote the regulation of body energy intake. Congenital hypothyroidism (CH) is a systemic metabolic disorder where T3 and T4 production during neonatal period is insufficient. CH due to dyshormonogenesis is a disease caused by inborn errors in T3 and T4 synthesis, with autosomal recessive inheritance. Mutations in NIS, SLC26A4, DUOX2, DUOXA2, TPO, TG and DEHAL-1 genes have been described. The iodide organification defect (IOD) is the most common cause of dyshormonogenesis, being the TPO defect the most frequent, followed by defects in DUOX2 and DUOXA2 proteins. TPO is responsible for iodide oxidation, tyrosine iodination and its coupling. Seventy mutations have been described throughout the gene. As a heme peroxidase, TPO requires H2O2 to its regular function. The main catalytic core for H2O2 generation in thyroid is the DUOX2/DUOXA2 complex. Twenty five mutations have been described in DUOX2 gene and only one mutation in DUOXA2 gene. In our previous study, we evaluated patients with CH after 3 years of age to establish their etiologic diagnosis, by combining serum TG, thyroid ultrasound, and radioiodide uptake with 131I. Seven patients were diagnosed with IOD. In these patients, we evaluated TPO gene and identified several already described SNPs. One patient had the p.Q660E mutation in heterozygous state, another patient had the SNP p.R584Q in homozygous state and a third one had p.Q660E and p.584Q in compound heterozygous state. The aims of this study were to search for mutations in DUOX2 and DUOXA2 genes in patients with IOD and perform a functional study of TPO p.R584Q change. For the molecular study, DNA was extracted from peripheral blood leukocytes of each patient and parents, followed by PCR, and automatic sequence, and the results were compared with normal sequences of each gene (GenBank). For functional analysis of TPO p.R584Q, HeLa cells were transfected with pcDNA plasmids containing normal and altered TPO gene and the protein activity was assessed by AmplexRed system. In silico analyzes were performed with the bioanalysis programs: PolyPhen, MutationTaster, SIFT and PSIPRED. At the end of the molecular study, in DUOX2 gene we identified 20 previously described SNPs, including the functional p.H678R SNP (rs57659670), present in heterozygous state in 3 patients. We also identified the new p.A1087V change in heterozygous state in one patient. According to bioassay programs datas, p.A1087V change is damage and p.H678R SNP is tolerable. In DUOXA2 gene we identified five previously described polymorphisms and no mutation. In TPO functional study, we observed a significant activity decrease of TPO p.R584Q compared to normal TPO (5% of activity; p=0.0193). According to bioassay programs datas, p.R584Q is damaging. Three patients showed no changes in TPO, DUOX2 and DUOXA2 genes studied regions. A review of clinical and laboratory data suggested the presence of other altered proteins, such as TG, Pendrin or TSH receptor. One patient had the new DUOX2 p.A1087V alteration in heterozygous state and no other changes in the studied regions of evaluated genes, suggesting that there could be changes in other nonevaluated regions or the monoallelic expression of DUOX2. The functional DUOX2 p.H678R SNP was identified in three patients with changes in TPO: one with p.R584Q change in homozygous state and another one with p.R584Q and p.Q660E in compound heterozygous state. These cases have the two alleles of TPO changed, justifying their IOD. A third case showed only the TPO p.Q660E mutation in heterozygous state. We speculate that the patient may present changes in regions nonevaluated or the monoallelic expression of TPO. We conclude that we defined the molecular diagnosis of four patients, that showed significant changes in evaluated genes, and that TPO p.R584Q change is functionally harmful, causing IOD

An ideal biosensor is a compact and in-expensive device that is able to readily and rapidly detects different types of analytes with high sensitivity and specificity. The affectability of a biosensing methodology is subject to the limit of nanomaterials to transduce the target binding process to an improved perceptible signal, while the selectivity is accomplished by considering the binding and specificity of certain moieties to their targets. Keeping these requirements in mind we have chosen nanomaterials such as carbon nanotubes (CNTs) and gold nanoparticles (AuNPs) that has catalytic properties combined with their size, shape and configuration dependent chemical and physical properties as essential precursors and signaling components for creation of biosensors with tremendous sensitivity. The primary goal of the research work described in this dissertation is to develop and evaluate novel methods to detect various analytes using nanomaterials, at the same time making an affordable architecture for point-of-care (POC) applications. We report here in chapter 3 a simple and new strategy for preparing disposable, paper-based, porous AuNP/M-SWCNT hybrid thin gold films with high conductivity, rapid electron transfer rates, and excellent electrocatalytic properties to achieve multiple analyte electrochemical detection with a resolution that greatly exceeds that of purchased flat gold slides. We further explored the use of nanomaterial-based paper films in more complex matrices to detect analytes such as NADH, which can act as a biomarker for certain cellular redox imbalances and disease conditions. Carbon nanotubes with their large activated surfaces and edge-plane sites (defects) that are ideal for performing NADH oxidation at low potentials without any help of redox mediators minimizing surface fouling in complex matrices is described in chapter 4. With an instrument-free approach in mind we further focused on a colorimetric platform using split cocaine aptamers and gold nanoparticles (AuNPs) to detect cocaine for on-site applications as described in chapter 5. In chapter 5, the split aptamer sequences were evaluated mainly on three basic criteria, the hybridization efficiency, specificity towards the analyte (cocaine), and the reaction time to observe a distinguishable color change from red to blue. The assay is an enzyme-assisted target recycling (EATR) strategy following the principle that nuclease enzyme recognizes probe–target complexes, cleaving only the probe strand releasing the target for recycling. We have also studied the effect of the number of binding domains with variable chain lengths on either side of the apurinic (AP) site. On the basis of our results, we finally shortlisted the sequence combination with maximum signal enhancement fold which is instrumental in development of colorimetric platform with faster, and specific reaction to observe a distinctive color change in the presence of cocaine.

The sodium-dependent NADH-ubiquinone oxidoreductase (Na⁺-NQR) was discovered first in the marine bacterium, Vibrio alginolyticus. It acts as a primary electrogenic pump for sodium translocation during aerobic respiration, generating a sodium motive force which drives ATP synthesis, solute transport and flagellar motion. Early biochemical studies indicated that Na⁺-NQR was composed of 3 subunits: α, β and γ, with apparent M_r values of 52, 46 and 32 kDa. A proposed model suggested that the β subunit, a NADH dehydrogenase, accepts electrons from NADH and reduces menadione or quinone by a Na⁺-independent one-electron transfer reaction to produce the semiquinone. The subsequent reduction of the semiquinone is dependent on Na⁺ and is catalyzed by the α subunit. Degenerate oligonucleotides designed from the N-terminal sequences obtained from partially purified α and γ subunits were used to isolate clones from an EcoRI library of wild-type V. alginolyticus DNA. Six genes which comprise the nqr operon, nqrA-nqrF, were sequenced and identified. Sequence analysis and database comparisons led to the conclusion that this enzyme complex is both structurally and evolutionarily distinct from the H⁺-translocating NADH-ubiquinone oxidoreductase. Na⁺-NQR comprises 3 hydrophilic subunits, NqrA, NqrC and NqrF and 3 highly hydrophobic membrane-spanning subunits, NqrB, NqrD and NqrE. The 3 hydrophilic subunits, NqrA, NqrC and NqrF correspond to the previously identified α, γ and β subunits respectively. Based on sequence comparisons, a [2Fe-2S] cluster region, a FAD binding site and an NADH binding domain were identified in NqrF, the proposed NADH dehydrogenase subunit. From hydropathy plots, NqrF also appeared to possess a hydrophobic N-terminal region. Pulse-chase radiolabelling of various clones expressing nqrB-nqrF verified that the putative products of the nqr operon identified from sequencing, were indeed transcribed and translated in vivo. The nqrF gene was cloned into pET16-b and expressed in Escherichia coli, BL21(DE3)pLysS as a 46 kDa polypeptide.

Plant mitochondrial genomes are known to undergo frequent DNA rearrangements during evolution. Such DNA rearrangements have been observed within the extreme 5' or 3' termini of plant mitochondrial genes. The present studies of the gene for NADH dehydrogenase subunit I (nad1) in wheat demonstrate that DNA rearrangements can even occur at internal sites. This work shows that the nad1 gene is comprised of five single-copy exons in wheat mitochondria. The predicted NAD1 amino acid sequence is closely related to that from non-plant and chloroplast counterparts. Somewhat surprisingly, these nad1 sequences are scattered at four distantly-separated sites in the wheat mitochondrial genome. The analysis of regions flanking nad1 coding segments revealed the presence of sequence motifs and helical structures that are hallmarks of group II introns. A model is proposed for nad1 gene expression in which one cis- and three trans-splicing events are necessary for the production of nad1 mRNAs. To investigate nad1 gene expression at the RNA level, transcripts arising from the four nad1 coding regions were analyzed. Northern blot hybridizations and cDNA sequence analysis show that stable transcripts contain all five correctly-linked nad1 exons. S1 nuclease analysis in the regions flanking the nad1 coding segments also revealed the presence of stable transcripts which would be large enough to contain group II intron structures of normal sizes (<3 kb). As has been observed for virtually all plant mitochondrial mRNAs, the maturation of nad1 transcripts also involves RNA editing events. Interestingly, one of these RNA editing sites converts an ACG codon to AUG to create an initiation codon, and this suggests that RNA editing at this site is obligatory for translation of nad1 mRNAs to proceed. RNA editing is also observed within the discontinuous nad1 a/b intron in wheat (which is of particular interest because it lacks several key features of group II introns) but any contribution to intron structure or splicing is as yet uncertain. The wheat nad1 gene organization seems to have resulted from DNA rearrangements that occurred within previously continuous introns. This organization of the nad1 gene in wheat, a monocot, differs from that of dicot nad1 genes and this suggests that some DNA rearrangements have occurred relatively recently during plant evolution. The unusual nad1 gene structure shows that DNA rearrangements can alter not only gene order but also gene structure, provided that scattered gene pieces are properly transcribed and spliced.

The ADP-ribose elongation catalyzed by poly(ADP-ribose) polymerase (PARP) [EC 2.2.2.30] has been partially characterized utilizing mono (ADP-ribosyl)ated polyamines. Arginine methyl ester (AME)-(ADP-ribose) and agmatine (AGMT)-(ADP-ribose) were synthesized enzymatically with a eukarytic mono(ADP-ribosyl) transferase and cholera toxin, respectively.

Leishmania are protozoan parasites that are transmitted by a sand fly vector. These parasites affect not only humans but also wild animals including domestic dogs and rodents, which form an additional challenge and public health problem to control the disease. Leishmaniasis is an important disease with worldwide distribution, including Saudi Arabia, the Middle East, and other tropical and subtropical areas around the world. Due to the expansion of irrigation and agricultural activities, more exposure to sand fly occurs, which leads to the expansion of leishmaniasis infections as newly emerging disease. Emerging drug resistance in leishmaniasis is an additional problem, contributed by enzymes involved in the detoxification of pharmacological agents and other xenobiotics. Cytochrome b5 reductase (Cb5r) has a high pharmacological significance because of its essential role in fatty acid elongation, biosynthesis of cholesterol (humans) or ergosterol (Leishmania, fungi), and cytochrome P450-mediated detoxification of xenobiotics. Leishmania Cb5r has seven different isoforms whereas human has only one. Cb5r-7 isoform in Leishmania has closest homology to the human Cb5r. The three specific aims of this thesis project are focusing on (i) cloning of the Cb5r-7 isoform from Leishmania mexicana, (ii) its purification as recombinant His-tagged protein from E.coli, and (iii) its functional characterization as potential pharmacological target against Leishmania.

Die vorliegende Arbeit behandelte den Einfluss von membran-assoziierten Faktoren im Hippocampus auf das axonale Wachstum, zum einen während der Entwicklung des entorhino-hippocampalen Systems und zum anderen nach Deafferenzierung des adulten Hippocampus. Mit Hilfe des Streifenassays und des Längenauswachsassays wurden zuerst die maturationsabhängigen Eigenschaften von membran-assoziierten Faktoren im Hippocampus getestet. Es zeigte sich, dass entorhinale Axone zwischen ihrem normotypischen Zielgebiet und Kontrollregionen diskrimieren können und bevorzugt auf Membranen ihres Zielgebiets wachsen. Im Folgenden wurden dann Axonen hippocampale Membranen unterschiedlicher Entwicklungsstadien im Streifenassay angeboten. In diesem experimentellen Ansatz wuchsen entorhinale Axone präferenziell auf jenen hippocampalen Membranen, die aus dem Entwicklungsstadium stammen, in den die entorhinalen Fasern in vivo in den Hippocampus einwachsen. Diese Experimente ergaben, dass das in vivo zeitlich genau regulierte Einwachsen entorhinaler Fasern in den Hippocampus von membran-assoziierten Faktoren determiniert ist und ein Zeitfenster für das Vorhandensein dieser Faktoren im Hippocampus existiert. Eines der wesentlichen Charakteristika der Maturation des zentralen Nervensystem ist die Bildung von Myelin und die Myelinisierung von Fasertrakten. Immunozytochemische Analysen mit Myelin-spezifischen Markern ergaben, dass dieses maturationsabhängige Auswachsverhalten zeitlich gut mit der Myelinisierung dieser Hirnregion korreliert. Eine Reihe von in vivo und in vitro Experimenten verschiedener Arbeitsgruppen demonstrierten, dass Myelin starke auswachsinhibitorische Eigenschaften hat, die sogar den Kollaps von Wachstumskolben induzieren können. In Längenauswachsassays zeigte sich, dass Myelin einen starken inhibitorischen Effekt auf das Längenwachstum von entorhinalen Axonen hat. Mit physikalischen Separationstechniken und unter Verwendung des funktionellen Antikörpers gegen inhibitorische Myelinproteine (IN-1) konnte dieser Effekt neutralisiert werden und das neuronale Längenwachstum war wieder vergleichbar zur Kontrollsituation. Untersuchungen im Streifenassay ergaben zusätzlich, dass das wachstumsinhibitorische Myelin und seine Komponenten keine axonalen Lenkungseigenschaften hatte und die gerichtete Zielfindung axonalen Auswachsens nicht beeinflusst. In weiteren Experimenten wurden die membran-assoziierten Faktoren im deafferenzierten Hippocampus untersucht. Dabei zeigte sich, dass nach einer Läsion wachstumsfördernde Faktoren in hippocampalen Membranen vorliegen. Zusätzlich liegen in einem engen Zeitfenster axonale Lenkungsmoleküle vor mit vergleichbarer Attraktivität für entorhinale Axone, wie sie aus entsprechenden Entwicklungsstadien bekannt sind. Die Experimente lassen den Schluss zu, dass im deafferenzierten Hippocampus Faktoren läsionsinduziert werden, und dass diese Faktoren membran-assoziiert sind. Es wird seit langem angenommen, dass das ZNS von adulten Vertebraten in seinem zellulären Zustand determiniert ist und zu keinen grösseren plastischen Veränderungen fähig ist. Gerade nach einer Schädigung von adultem ZNS ist die Regenerationsfähigkeit im Unterschied zu jungen, postnatalen ZNS sehr eingeschränkt. Die beschränkte Regenerationsfähigkeit des adulten ZNS ist wesentlich determiniert durch die Präsenz des auswachsinhibitorischen Myelins. Nichtsdestotrotz gibt es kompensatorisches Sprouting im Hippocampus, die verlorengegangene synaptische Kontakte ersetzen. Die Identifizierung der Faktoren, die das schichten-spezifische Einwachsen aussprossender Axone kontrollieren, trägt wesentlich zum Verständnis dieses Phänomens bei. Weiterhin wird die Aufklärung der zugrundeliegenden molekularen Faktoren für die spezifische Zielerkennung und deren Charakterisierung uns helfen, das Potential und die Limitation der Regeneration im ZNS besser zu verstehen und die Möglichkeit eröffnen, einmal verlorengegangene neuronale Verbindungen durch therapeutische Intervention wieder spezifisch aufzubauen.
In this study, the impact of membrane-associated factors on axonal outgrowth during development and following lesion was examined. We studied the maturation-dependent features of membrane-associated molecules in the hippocampus with the stripe assay for guidance activity and with the outgrowth assay for outgrowth-supporting activity. We could show that entorhinal axons discriminate between their proper target area, the hippocampus, and control regions which do not receive synaptic connections from the entorhinal cortex, and preferred to grow on hippocampal membranes. Further, we examined guidance preferences of entorhinal neurites on hippocampal membranes in different developmental stages. The choice behavior of entorhinal neurites for hippocampal membranes temporally correlates with the ingrowth of the perforant path into the hippocampus and with the stabilization of this brain area in vivo, and further indicate the transient presence of membrane-associated guidance cues in the hippocampus. One of the characteristics of maturational processes in the central nervous system is the developmentally regulated myelination of fiber tracts. Comparison of the stripe assay data with immunohistochemical analysis for MBP and MAG as representative myelin markers revealed a correlation between the changes in axonal choice behavior and increasing myelination. It is known that myelin itself is a strong axonal outgrowth inhibitor and that myelin can also induce growth cone collapse. In outgrowth assays, we could show that myelin has a strong outgrowth inhibitory influence on entorhinal axons which can be neutralized by the monoclonal antibody IN-1. However, in the stripe assay, myelin did not influence the choice behavior of outgrowing axons and this indicates that myelin does not govern information for directed growth. Furthermore, stripe assays were performed with membranes obtained from deafferented hippocampi at various lesion stages. In these experiments, we could show that outgrowth-promoting factors are present in the lesioned hippocampus. Moreover, data from the stripe assay revealed the timely restricted presence of membrane-bound guidance factors which are equally as attractive as neonatal hippocampal membranes. These experiments indicate the lesion-induced expression of outgrowth-promoting factors in the hippocampus, which correlates temporally with the sprouting reaction in vivo. It is suggested that the central nervous system of adult vertebrates is determined in its cellular condition and not capable of structural changes. This is most evident following lesion of adult brain, where the ability for regeneration is highly restricted in comparison to young, postnatal neural tissue. This restricted ability for regeneration in the adult brain is essentially determined by the presence of outgrowth-inhibitory myelin. However, a compensatory sprouting response exists in the adult hippocampus following lesion, which leads to a layer-specific replacement of lost synaptic contacts. The identification of these factors will lead to a deeper understanding of layer-specific axonal sprouting and synaptic replacement. Further, the identification and characterization of the underlying factors will help us to understand the potential and limitations of regeneration in the central nervous system.

Pioglitazone (PGZ) is a peroxisome proliferator-activated receptor (PPAR)-γ agonist that improves peripheral insulin sensitivity and reduces hepatocellular injury/ inflammation in non-alcoholic steatohepatitis (NASH). However, the underlying hepatic mechanism of action is not clearly understood with PGZ treatment. Therefore, liver biopsies were used to study genes, protein and immunohistochemistry expression of hepatocyte and hepatic stellate cell markers. PGZ decreased both αSMA and PPAR β expression in stellate cell and PPAR α hepatocyte expression, hence inhibit both stellate cell activation and β-oxidation in hepatocytes. PGZ also inhibit cell proliferation by reducing both PCNA and Ki67 in the liver. Up regulation of PPAR β, PXR, LXRα, IkBα and TNFRSF1B were observed (using Taqman Low density array gene expression), which indicates that PGZ exerts an anti-inflammatory and anti-fibrotic effect. PPAR β, PGC1α, ACADVL and UCP2 up regulation lead to increase β-oxidation and reduced reactive oxygen species (ROS) production. LXRα, ChREBP and SREBP1C activation leads to lipogenesis in the liver was also observed in PGZ treatment group. In vitro study was also conducted in freshly isolated human hepatic stellate cells, where these cells were incubated in vehicle and 5μM of PGZ for 72 hours consecutively. After 24 hours, 15ng/ml of PDGF-BB was incubated for 48 consecutive hours, followed by cell proliferation and gene expression analysis. PGZ up regulate the adipogenic genes expression followed by reduction in stellate cells marker expression and cell proliferation induced by PDGF-BB. PPAR β elevation after PGZ treatment in human liver and HSCs culture are novel findings in this study, but the role of PPAR β is clearly unknown in the liver and stellate cells. Therefore, similar treatment was performed using PDGF-BB on freshly isolated human HSCs, followed by treatment with PPAR β agonist (GW0742). GW0742 restores the adipogenic genes expression maintaining the quiescent phenotype of the stellate cell in contrast to previous study where PPAR β has been reported to cause stellate cells activation and proliferation. Overall, PGZ improved injury and fibrosis, inhibiting cell proliferation, increased both lipogenesis and β-oxidation in NASH patients. PGZ also inhibit stellate cells activation and proliferation and up regulated the adipogenic genes.

CHARACTERIZATION OF STAPHYLOCOCCAL NUCLEASE AND TUDOR DOMAIN CONTAINING PROTEIN 1 (SND1) AS A MOLECULAR TARGET IN HEPATOCELLULAR CARCINOMA AND NON-ALCOHOLIC STEATOHEPATITIS Nidhi Jariwala, PhD A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Integrative Life Sciences Virginia Commonwealth University, 2017 Devanand Sarkar, M.B.B.S., PhD. Associate Professor, Department of Human and Molecular Genetics Virginia Commonwealth University Richmond, Virginia SND1, a subunit of the miRNA regulatory complex RISC, has been implicated as an oncogene in hepatocellular carcinoma (HCC). Oncoprotein SND1 regulates gene expression at a post-transcriptional level in multiple cancers including hepatocellular carcinoma (HCC). In the present study, we characterize oncogenic functions of SND1 in HCC employing a novel transgenic mouse model (Alb/SND1) and present SND1 as a potential molecular target in HCC management. We show that Alb/SND1 mice develop spontaneous HCC with partial penetrance and exhibit more highly aggressive HCC induced by chemical carcinogenesis. Livers from Alb/SND1 mice exhibit a relative increase in inflammatory markers and spheroid-generating tumor initiating cells (TiC). Mechanistic investigations defined roles for Akt and NF-κB signaling pathways in promoting TiC formation in Alb/SND1 mice. Intravenous administration of the selective SND1 inhibitor 3', 5'-deoxythymidine bisphosphate (pdTp) inhibited tumor formation without effects on body weight or liver function. We conclude that SND1 drives pro-oncogenic transcriptomic and proteomic changes in hepatocyte resulting in aggressive HCC. SND1 specific RNA interactome is identified with RNA immunoprecipitation sequencing (RIPSeq) approach. With an adjusted p value of2-fold enrichment over control, 282 mRNAs were identified to significantly associate with SND1 protein. We focused on the tumor suppressor Protein Tyrosine Phosphatase non-receptor type 23 (PTPN23) because its regulation by SND1 and its role in HCC are not known. In current study, we confirm that SND1 post-transcriptionally downregulates PTPN23. Pursuing functional studies with tetracycline inducible overexpression system, we validate that PTPN23 inhibits tyrosine kinase signaling, proliferation, epithelial to mesenchymal transition, migration, invasion and in vivo tumorigenesis. Alb/SND1 mice also manifest steatosis and fibrosis at one year of age. Coupled with a pro-inflammatory hepatic phenotype, we conclude that Alb/SND1 livers present NASH. High fat diet causes severe NASH and aggressive NASH induced HCC in Alb/SND1 mice. Serum and hepatic lipid profiling shows that hepatocyte specific SND1 overexpression associate with elevated triglyceride and cholesterol LDL levels. Contrarily, hepatocyte specific deletion of SND1 (SND1ΔHEP) in vivo, significantly protects against age dependent steatosis. Association of SND1 in NASH pathology is novel discovery and we present preliminary evidence confirming role of SND1 in promoting NASH.

The CO dehydrogenase~linked ferredoxin from acetate-grown Methanosarcina thermophiIa was characterized to determine the structure and biochemical properties of the iron-sulfur clusters. Chemical and spectroscopic analyses indicated that the ferredoxin contained two [4Fe-4S] clusters per monomer of 6,790 Da, although a [3Fe-4S] species was also detected in the oxidized protein. The midpoint potentials of the [4Fe-4S] and [3Fe~4S] clusters at pH 7 were -407 m V and + 103 m V, respectively. Evidence from biochemical and spectroscopic studies indicated that the [3Fe-4S] species may have been formed from [4Fe-4S] clusters when ferredoxin was oxidized. The gene encoding the CO dehydrogenase-linked ferredoxin (fdxA) in Ms. thermophila had the coding capacity for a 6,230-Da protein which contained eight cysteines with spacings typical of 2[4Fe-4S] ferredoxins. A second open reading frame (ORF1) was also identified which had the potential to encode a 2[4Fe-4S] bacterial-like ferredoxin (5,850 Da). The deduced proteins from fdxA and ORF1 were 62% identical. fdxA and ORFI were present as single copies in the genome and each was transcribed on a monocistronic mRNA. Both fdxA and ORF1 were transcribed in cells grown on methanol and trimethylamine, but only the fdxA -specific transcript was detected in acetate-grown cells. The apparent transcriptional start sites of fdxA and ORFI were downstream of sequences which had high identity with the consensus methanogen promoter. The heterodisulfide of two cofactors unique to the methanogenic microorganisms, HS-HTP and HS-CoM, was enzymatically reduced in cell extracts of Ms. thermophila using electrons from the oxidation of either H₂ or CO. The homodisulfides of either HS-HTP or HS-CoM were not reduced under the same conditions. The results indicated that methane is formed by reductive demethylation of CH₃-S-CoM using HS-HTP as a reductant in Ms. thermophila. Coupling of CO oxidation with reduction of the heterodisulfide suggested that the CO dehydrogenase-linked ferredoxin may be involved, although the details of electron flow are not known.
Ph. D.

Nox1 is of considerable importance because of its involvement in a wide variety of pathologies. Activation of Nox1 induces generation of reactive oxygen species (ROS) and cell migration, events critical for the pathogenesis of cardiovascular disease, amyotropic lateral sclerosis, gastrointestinal disease, immunological disorders, and multiple forms of cancer [1-8]. In order to best determine how to treat Nox1-mediated disease, we must gain a better understanding of the mechanisms that control Nox1 activation. Within the last decade, many studies have found that protein phosphorylation and protein trafficking are critical regulatory mechanisms that control the activation of multiple Nox proteins. Yet, to date, no studies have characterized Nox1 phosphorylation or trafficking. We hypothesized that the activity of Nox1 is controlled by its phosphorylation at specific residues and by its sub-cellular localization; and that modifying Nox1 phosphorylation or localization will alter Nox1-dependent signaling. To test this hypothesis, we utilized both in vivo and in vitro approaches. We found that phosphorylation of Nox1 is significantly increased under pathological conditions in three in vivo models: (1) in atherosclerotic vs. normal aorta from monkey, (2) in neointimal vascular smooth muscle cells (VSMCs) vs. medial VSMCs from rat following aortic balloon injury, and (3) in ligated vs. normal carotid from mouse. Studies using mass spectroscopy, pharmacological inhibition, siRNA, and in vitro phosphorylation identify PKC-βI as a kinase that mediates Nox1 phosphorylation and subsequent ROS production and VSMC migration. Site-directed mutagenesis of predicted Nox1 phospho-residues revealed that cells expressing mutant Nox1 T429A have a significant decrease in TNF-α-stimulated ROS production, VSMC migration and Nox1 NADPH oxidase complex assembly compared to cells expressing wild-type Nox1. Isothermal calorimetry (ITC) revealed that a peptide containing the Activation Domain of NoxA1 (LEPMDFLGKAKVV) binds to phosphorylated Nox1 peptide (KLK-phos-T(429)- QKIYF) but not non-phosphorylated Nox1 peptide. These findings indicate that phosphorylation of Nox1 residue T429 by PKC-βI promotes TNF-α-induced Nox1 NADPH oxidase complex assembly, ROS production, and VSMC migration. Nox1 localization and trafficking studies reveal that Nox1 endocytosis is necessary for TNF-α-induced Nox1 ROS production; and that mutation of a Nox1 VLV motif inhibits Nox1 endocytosis and ROS production. These studies have provided new evidence that phosphorylation and sub-cellular localization are involved in the regulation of Nox1 ROS production and cell migration and offer new insights as to how Nox1 activity can be targeted for the purpose of treating Nox1-mediated diseases.

Note: Portions of this abstract have been previously published in the journal Blood, Basiorka et al. Blood. 2016 Oct 13, and has been reproduced in this manuscript with permission from the publisher. Myelodysplastic syndromes (MDS) are genetically diverse hematopoietic stem cell malignancies that share a common phenotype of cytological dysplasia, ineffective hematopoiesis and aberrant myeloid lineage maturation. Apoptotic cell death potentiated by inflammatory cytokines has been considered a fundamental feature of MDS for over two decades. However, this non-inflammatory form of cell death cannot account for the inflammatory nature of these disorders. We report that a hallmark of lower-risk (LR) MDS is activation of the NLRP3 inflammasome, which drives clonal expansion and pyroptosis, a caspase-1-dependent programmed cell death induced by danger-associated molecular pattern (DAMP) signals. Independent of genotype, MDS hematopoietic stem and progenitor cells (HSPC) overexpress pyroptosis-related transcripts, inflammasome proteins and manifest activated NLRP3 inflammasome complexes that direct caspase-1 activation, IL-1β and IL-18 maturation and pyroptotic cell death. Using the S100A9 transgenic (S100A9Tg) mouse model that phenocopies human MDS, we demonstrated that forced expression of S100A9 was sufficient to drive pyroptosis in vivo, implicating pyroptosis as the principal mechanism of HSPC cell death in S100A9Tg mice. The lytic cell death releases intraceullar contents that include alarmins and catalytically active ASC specks, which can propagate bystander inflammation. Notably, MDS mesenchymal stromal cells (MSC) and stromal-derived linages were found to predominantly undergo pyroptosis, with marked activation of caspase-1 and NLRP3 inflammasome complexes. These findings may account for the clusters of both HSPC and stromal cell death previously described in the bone marrows of patients with MDS. Mechanistically, pyroptosis is triggered by the alarmin S100A9 that is found in excess in MDS HSPC and bone marrow (BM) plasma. Further, both somatic gene mutations and S100A9-induced signaling activate NADPH oxidase (NOX), generating reactive oxygen species (ROS) that initiate cation influx, cell swelling and β-catenin activation. Accordingly, ROS and active β-catenin were significantly increased in MDS BM mononuclear cells (BM-MNC) and S100A9Tg mice compared to normal controls, as well as in human cell lines harboring gene mutations and in murine models of gene mutation knock-in or gene loss. ROS and β-catenin nuclear translocation were significantly reduced by NLRP3 or NOX inhibition, indicating that S100A9 and somatic gene mutations prime cells to undergo NOX1/4-dependent NLRP3 inflammasome assembly, pyroptosis and β-catenin activation. Together, these data explain the concurrent proliferation and inflammatory cell death characteristic of LR-MDS. Given that loss of a gene-rich area in del(5q) disease results in derepression of innate immune signaling, we hypothesized that this genetic deficit would trigger assembly of the NLRP3 inflammasome complex, akin to the pathobiological mechanism characteristic of non-del(5q) MDS. To this end, we utilized two distinct murine models of del(5q) disease, namely in the context of Rps14 haploinsufficiency and concurrent loss of mDia1 and microRNA (miR)-146a. In both models, pyroptosis was not evident in the HSPC compartment; however, early erythroid progenitors displayed high fractions of pyroptotic cells. This was associated with significant increases in caspase-1 and NLRP3 inflammasome activation, ROS and nuclear localization of β-catenin, which was extinguished by inflammasome or NOX complex inhibition. These data suggest that early activation of the inflammasome drives cell death and prevents terminal maturation of erythroid precursors, accounting for the progressive anemia characteristic of del(5q) disease, whereby hematopoietic defects are primarily restricted to the erythroid compartment. Importantly, these data implicate a similar pathobiological mechanism in del(5q) MDS as is observed in non-del(5q) patients. The identification of the NLRP3 inflammasome as a pathobiological driver of the LR non-del(5q) and del(5q) MDS phenotype allows for novel therapeutic agent development. Notably, knockdown of NLRP3 or caspase-1, neutralization of S100A9, and pharmacologic inhibition of NLRP3 or NOX suppresses pyroptosis, ROS generation and nuclear β-catenin in MDS, and are sufficient to restore effective hematopoiesis. In del(5q) murine models, inhibition of the NLRP3 inflammasome significantly improved erythroid colony forming capacity by a mechanism distinct from that of lenalidomide, highlighting the translational potential for targeting this innate immune complex in this subset of MDS. Thus, alarmins and founder gene mutations in MDS license a common redox-sensitive inflammasome circuit, which suggests new avenues for therapeutic intervention. Furthermore, aggregated clusters of the NLRP3 adaptor protein ASC [apoptosis-associated speck-like protein containing a caspase activation and recruitment domain (CARD)] are referred to as ASC specks. During pyroptosis, ASC specks are released from dying cells and function as DAMP signals that propagate inflammation. In this way, specks are a surrogate marker for NLRP3 inflammasome activation and pyroptotic cell death. Given that pyroptosis is the predominant mechanism of cell death in MDS and ASC specks are readily quantified by flow cytometry, we hypothesized that BM or peripheral blood (PB) plasma-derived ASC specks may be a biologically rational biomarker for the diagnosis of MDS. The percentage of ASC specks were significantly increased in MDS BM plasma compared to normal, healthy donors, which was validated by confocal microscopy. PB plasma-derived ASC specks were significantly greater in LR- versus HR-MDS, consistent with the greater extent of cell death and myeloid-derived suppressor cell (MDSC) expansion in LR disease. As hyperglycemia induces NLRP3 inflammasome activation, plasma glucose levels were measured to adjust for this confounding variable. Subsequently, the percentage of glucose-adjusted, PB plasma-derived ASC specks was measured in a panel of specimens of varied hematologic malignancies. The corrected percentage of ASC specks was significantly increased in MDS compared to normal donors and to each other malignancy investigated, including other myeloid and lymphoid leukemias, myeloproliferative neoplasms and overlap syndromes, like chronic myelomonocytic leukemia (CMML). These data indicate that the glucose-adjusted ASC speck percentage is MDS-specific and may be a valuable diagnostic biomarker. At a cutoff of 0.039, the biomarker minimizes misclassification error and achieves 95% sensitivity and 82% specificity in classifying MDS from normal donors, other hematologic malignancies and T2D. Lastly, the biomarker declined with treatment response to lenalidomide in LR-MDS patients, but not to erythropoietin stimulating agent (ESA) or hypomethylating agent (HMA) therapy. As such, the percentage of ASC specks represents the first biologically rational, diagnostic biomarker for MDS that can be implemented with current diagnostic practices to reduce diagnostic error.

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Temperature can interfere with protein structure and function, affecting its ability to bind to other molecules, its conformational microstates distribution, as well as the rate of its enzymatic reactions. Since the mid-20th the in silico or computer experiments have increasingly been used in different areas of science to help better understand and prove theoretical hypotheses. In this context, molecular dynamic (MD) simulations, a computational molecular biophysics technique was used in the study of structural variations in the native state of proteins as well as in the design and development of new drugs. The focus of the present study is on the effect of temperature in the enzyme 2-trans-enoil-ACP (CoA) reductase (InhA) from Mycobacterium tuberculosis by means of MD simulations. The InhA enzyme is the bonafide target of isoniazid (INH), the most important medicine used in the treatment of tuberculosis. The InhA-NADH enzymatic complex was submitted to MD simulations at 25 oC (298 K) and at 37 oC (310 K) for a total simulation time of 20 ns each. The temperature of 37 oC was chosen because it is the human body temperature, whilst 25 oC is used in in vitro experiments under normal conditions of temperature and pressure (NTP). Structural parameters such as root-mean square deviation or RMSD, radius of gyration, B-factors, and solvent accessible surface area were calculated from the MD trajectories. There are statistically significant conformational differences between the 3D structures resulting from 25 ºC and 37 ºC MSD. We also investigated the effect of temperature in the molecular flexibility. While observing a significant increase in flexibility in the substrate binding region (A- and Bloops and in the substrate biding loop), at 37 ºC the helices α6, α7 and α2 presented low B-factors at human body temperature. In the NADH coenzyme binding site, only three residues (Ser20, Ile21 e Phe41) presented lower flexibility with temperature increase. Small increases in temperature significantly affect the protein conformation in important regions that are relevant to its function. The increase in temperature changes the protein flexibility but in a heterogeneous way, preserving regions that need more stability in the functional aspect. The clear changes in the InhA enzyme and its coenzyme NADH during the temperature increase process from 25 ºC to 37 ºC must be considered in planning new drugs against this target. Therefore, we should take into account the environmental conditions (air pressure, temperature and pH) which they will be submitted on in vivo. We suggest, for the future, that research of targets to be done in temperature equal or very close to body temperature and to the one used at the dynamic spectrum of these target structures in molecular docking experiments, an important step in rational drug design.
Esta pesquisa refere-se a um estudo computacional via simulação por dinâmica molecular (DM) que investiga os efeitos da temperatura na InhA, enzima 2-trans-enoil-ACP (CoA) redutase do Mycobacterium tuberculosis (MTB). A temperatura pode interferir na estrutura e função protéicas, na habilidade de ligação de uma proteína, na distribuição dos microestados, na conformação molecular média e nas reações enzimáticas. A partir do início do século XX, os experimentos in silico tem sido cada vez mais utilizados para auxiliar na compreensão e comprovação das hipóteses teóricas elaboradas em diversas áreas da ciência. Neste contexto, a simulação por dinâmica molecular (DM) tem sido uma das técnicas da biofísica molecular computacional utilizadas no estudo da variação das propriedades estruturais do estado nativo das proteínas e no planejamento e design de fármacos. Esta pesquisa investigou o efeito da temperatura sobre a enzima 2-trans-enoil-ACP (CoA) redutase (InhA) através de um estudo por simulação pela DM (SDM). A enzima InhA é um importante alvo para a isoniazida (INH), um dos fármacos utilizados no tratamento da tuberculose (TBC). O complexo enzimático InhA-NADH foi submetido a uma SMD a 25 ºC (298 K) e outra a 37 ºC (310 K) durante um período de 20 ns. A temperatura de 37 ºC foi escolhida por corresponder à temperatura corporal humana. Por outro lado, 25 ºC representa a temperatura ambiente utilizada nos experimentos realizados em condições normais de temperatura e pressão (NTP). Alguns parâmetros iniciais (desvio médio quadrático, raio de giro, superfície acessível ao solvente) foram obtidos a partir da análise dos dados das duas trajetórias. Existem diferenças conformacionais estatisticamente significativas entre as estruturas 3D resultantes das SDM a 25 ºC e 37 ºC. Também pesquisou-se o efeito da temperatura sobre a flexibilidade molecular. Enquanto observamos um importante aumento da flexibilidade na região de ligação do vi substrato (alça A, alça B e alça de ligação do substrato) aos 37 ºC, as hélices α6, α7 e α2 apresentaram Fatores-B menores na temperatura corporal humana. Na região do sítio de ligação da coenzima, apenas três resíduos (Ser20, Ile21 e Phe41) apresentaram uma menor flexibilidade com o aumento da temperatura. Pequenos aumentos de temperatura afetam significativamente a conformação de uma proteína em regiões importantes para o desempenho de suas funções. A elevação da temperatura aumenta a flexibilidade da estrutura protéica, porém de forma heterogênea, preservando regiões que necessitam de maior estabilidade no aspecto funcional. As nítidas modificações da enzima InhA e sua coenzima NADH durante um processo de alteração de temperatura de 25 ºC para 37 ºC devem ser consideradas no decorrer do planejamento e design de qualquer fármaco. O conhecimento detalhado das estruturas alvo, portanto, deve levar em conta as condições ambientais (pressão, temperatura, pH) às quais serão submetidas em in vivo. Sugerem-se, para o futuro, pesquisas com temperaturas maiores e trabalhos com docking.

A doença de Chagas, causada pelo parasita Trypanosoma cruzi, acomete entre 6 a 8 milhões de pessoas em todo o mundo. Conhecida como tripanossomíase americana, por ter sido considerada endêmica apenas na América Latina, esta doença, se espalhou para outros continentes devido aos movimentos migratórios se tornando um problema de sáude mundial. Estima-se que 56.000 novos casos e cerca de 12.000 mortes por complicações relacionadas à doença de Chagas anualmente. A quimioterapia disponível para o tratamento é composta apenas por dois fármacos, nifurtimox e benznidazol, no entanto são pouco eficazes na fase crônica da doença. Estes fármacos apresentarem, ainda, efeitos adversos graves e resistência por parte de algumas cepas do parasita. Diante deste panorama, é iminente a necessidade da busca de novos fármacos contra T. cruzi. Para a busca racional de novos quimiterapicos antiparasitários é fundamental a identificação e caracterização de vias metabólicas essenciais à sobrevivência dos parasitas. Assim, a enzima sirtuína 2 - Silent Information Regulator 2 (Sir2), tem importante papel para a infecção por T. cruzi, pois está totalmente envolvida no seu ciclo celular do parasita. Esta é uma enzima NAD+ dependente da classe III histona desacetilases, e se mostra como um interessante alvo bioquímico para o desenvolvimento de antichagásicos. A disponibilidade do sequenciamento genômico da Sir2 nos permite utilizar estratégias de planejamento de fármaco baseado no receptor (SBDD - Structure Based Drug Design) na identificação de candidatos a fármacos para essa doença. Entre as técnicas modernas de SBDD utilizadas, a triagem virtual possibilita identificar e selecionar inibidores enzimáticos potentes e seletivos para o alvo escolhido. Assim, neste trabalho, foi construído por meio da técnica de modelagem comparativa o modelo da enzima Sir2 de T. cruzi. Uma simulação por dinâmica molecular de 200ns, foi realizada para averiguar a estabilidade do modelo obtido. Diante da estabilização do modelo a partir de 100ns, o mesmo foi validado utilizando análise de clusters, RMSD (Root-mean-square Deviation) e análises de frequência de ligações de hidrogênio com o Cofator (NAD+) e os aminoácidos do sítio de catálise foram observadas, estes passos de simulação e validação foram realizados no programa DESMOND. Com o modelo robusto, os campos de interações moleculares (MIFs) foram gerados no programa GRID (Molecular Discovery v2.1) com o intuito de elucidar as regiões favoráveis a interação com a enzima em relação a propriedades físico-químicas da Sir2. A partir dos MIFs favoráveis a Sir2 de T. cruzi foi possível a construção de dois modelos farmacofóricos, o qual se baseou nas interações do Cofator (NAD+) e o sítio de catálise (Nicotinamida). O mesmo foi apliacdo como filtro para Triagem Virtual no programa UNITY da plataforma SYBYL X 2.0, utilizando os bancos de dados ZINC15 e GSK. A triagem resultou na seleção de 8 compostos candidatos a inibidores. Destes foram adquiridos 6 compostos por serem considerados mais promissores devido a complementariedade molecular. Estes foram testados contra a enzima de T. cruzi Sri2. Após o ensaio foi possível avaliar a potência de 4 compostos, sendo o composto CDMS-01 (IC50 = 39,9uM) o mais promissor que será submetido à processos de otimização molecular.
Chagas disease, caused by the parasite Trypanosoma cruzi, affects between 6 and 8 million people worldwide. Also known as American trypanosomiasis, because it is considered endemic only in Latin America, but has spread to other continents due to migratory movements. It is estimated that 56,000 new cases and about 12,000 deaths from complications related to Chagas disease annually. The chemotherapy available for treatment consists of only two drugs, nifurtimox and benznidazole, however these are poorly effective in the chronic phase. These drugs also have serious adverse effects and resistance from strains of the parasite. Faced with this scenario, the need to search for new drugs against T. cruzi is imminent. For the drug planning for new antiparasitic chemotherapics, the identification and characterization of metabolic pathways essential to the survival of parasites is fundamental. Therewith, the sirtuin 2 - Silent Information Regulator 2 (Sir2) enzyme has an important role for T. cruzi infection, since Sir2 in the parasite is totally involved in its cell cycle. This is an NAD+-dependent enzyme of class III histone deacetylases, and it shows an interesting biochemical target for the development of antichagasic. The availability of Sir2 genomic sequencing allows us to use SBDD (Structure Based Drug Design) strategies in identifying drug candidates for this disease. Among the modern techniques of SBDD used, virtual screening makes it possible to identify and select potent and selective enzyme inhibitors for the chosen target. The model of the T. cruzi Sir2 enzyme was constructed using the comparative modeling technique. A molecular dynamics simulation of 200ns was performed to ascertain the stability of the obtained model. Considering the stabilization of the model from 100ns, it was validated using cluster analysis, Root-mean-square Deviation (RMSD) and hydrogen bond frequency analyzes with Cofator (NAD+) and the amino acids of the catalysis site were observed, these simulation and validation steps were performed in the DESMOND program. With the robust model, the molecular interaction fields (MIFs) were generated in the GRID program (Molecular Discovery v2.1) in order to elucidate the regions favorable to the interaction with the enzyme in relation to the physicalchemical properties of Sir2. From the MIFs favorable to Sir2 of T. cruzi it was possible to construct two pharmacophoric models, which was based on the interactions of Cofator (NAD+) and the catalysis site (Nicotinamide). It was also applied as a Virtual screening filter in the UNITY program of the SYBYL X 2.0 platform, using the ZINC15 and GSK databases. Screening resulted in the selection of 8 inhibitor candidate compounds. Six compounds were obtained from the screening, because they were considered more promising, and were tested against T. cruzi Sri2 enzyme. After the assay it was possible to evaluate the potency of 4 compounds, the most promising compound being CDMS-01 (IC50 = 39.9 µM) that will be submitted to molecular optimization processes.

Especies reativas de oxigenio/nitrogenio (ERO/ERN) produzidas por neutrofilos atraves do complexo NADPH oxidase (Nox2) estao diretamente associadas as acoes deleterias surgidas quando a inflamacao escapa do controle da homeostase. A ativacao da NADPH oxidase de neutrofilos requer o acoplamento das subunidades citosolicas aos componentes de granulos e translocacao do complexo a membrana do fagossoma. A PDI (Proteina Dissulfeto Isomerase, EC 5.3.4.1) e uma chaperona envolvida no trafego proteico celular, sendo encontrada na superficie de diversas celulas procarioticas e eucarioticas. Trabalhos previos sugeriram que PDI pode ser um dos componentes responsaveis pela montagem de Nox2, facilitando o enovelamento correto das subunidades do complexo e/ou auxiliando o transito das subunidades ate a membrana do fagossoma. Neste trabalho foi testada a atividade de Nox2 de neutrofilos inflamatorios correlacionada a atividade redutase de PDI de membrana e o efeito do nitroxido 4-hidroxi-2,2,6,6-tetrametil-1-piperidiniloxil (Tempol) sobre esses processos. Neutrofilos dormentes apresentaram baixa atividade de PDI e nao foi detectado consumo de oxigenio associado ao sistema Nox2, conforme ensaios realizados com uso de um pseudo-substrato para PDI e monitoramento com eletrodo de Clark, respectivamente. Sob estimulo de forbol (PMA), os fagocitos consumiram quantidade significativa de oxigenio (6.5„b0.58 nmol.min-1) e apresentaram alta atividade de PDI, cerca de quatro vezes maior que as celulas dormentes. Quando os fagocitos foram previamente tratados com Tempol houve decrescimo dose-dependente da atividade de Nox2 (ED50: 45 ƒÝg/106 neutrofilos), em correlacao direta com o decrescimo da atividade de PDI. Testes com inibidores padroes de PDI (bacitracina e acido ditionitrobenzoico- DTNB) confirmaram que a inibicao de PDI determina decrescimo da atividade de Nox2, resultados obtidos atraves de ensaios espectrofotometricos (reducao de citocromo c, 550 nm) e quimioluminescentes (sistema luminol-peroxidase). Em conjunto, os resultados apontam que, simultaneamente a atividade de Nox2 em neutrofilos estimulados, ocorre atividade redutase de PDI, confirmando que essa chaperona esta diretamente associada a ativacao e/ou manutencao da atividade da oxidase fagocitaria. Adicionalmente, esse trabalho mostrou que o nitroxido Tempol e capaz de modular negativamente a atividade de Nox2, cujo efeito, ao menos em parte, e decorrente da inibicao de PDI, sugerindo um novo mecanismo anti-inflamatorio dos nitroxidos.
Protein disulfide isomerase (PDI, EC 5.3.4.1) is an ubiquitously expressed enzyme that catalyses the rearrangement of disulfide bonds in target proteins. Previous studies suggest that PDI, which is a chaperone involved in protein trafficking and translocates to the cell surface, may regulate the phagocytic NADPH oxidase complex (Nox2). This study examines whether the nitroxide 4-hydroxy-2,2,6,6-tetramethyl-1-piperidinyloxy (Tempol) inhibits the regulatory activity of PDI interconnected to Nox2 in inflammatory neutrophils. Phorbol-triggered superoxide anion release was correlated with the PDI reductase activity detected in neutrophils, as determined by oxygen consumption and cleavage of a fluorescent probe, respectively. Both events were significantly inhibited in a concentration-dependent manner when neutrophils were pre-treated with Tempol, which has an ED50 of 45 M. To substantiate that Tempol’s action on PDI activity is related to Nox2 downregulation, assays with the known PDI inhibitors bacitracin and dithionitrobenzoic acid were performed to confirm their ability to decrease the neutrophil respiratory burst. This study shows that Tempol’s inhibition of Nox2 activity is correlated with decreased PDI reductase activity at the neutrophil cellular membrane, suggesting a close association between the enzymes of activated phagocytes and pointing to a novel anti-inflammatory mechanism for Tempol.
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
Fundação de Amparo à Pesquisa do Estado de Minas Gerais - FAPEMIG

Human impact has led to degradation of different marine ecosystems, especially coastal, estuary and river environments, causing the decline of many marine fish populations. Among elasmobranchs one of the most threatened ones are sawfishes (Chondrichthyes, Pristidae), resulting extinct in many coastal areas around the world. In the Mediterranean Sea they occurred with two species, Pristis pristis and P. pectinata, until the second half of the last century. To better understand the baselines and the past distribution of sawfish populations, historical rostra available in the museum collections demonstrated to be value resource. This study aimed to identify new short genetic markers and a new functional amplification protocol suitable for the specific identification of ancient sawfish’s finds. A total of 78 rostra specimens, dated 1700-1900 and catalogued as unknown or Mediterranean origin, were collected from 10 European museums and were properly prepared for ancient DNA genetic analysis. Small fragments (118-266bp) of the mitochondrial COI and the NADH2 genes resulted to be useful for the taxonomic identification of 69 rostra at the species level. All the analyses computed in this study, NJ tree reconstruction, Automatic Barcode Gap Discovery, Characteristic Attribute analysis and P-distance computed between species, showed in full concordance the identification of four sawfish species: P. pristis, P. zijsron, P. pectinata and Anoxypristis cuspidata. A high frequency of mismatches was found between molecular identification and species museum cataloguing, especially between P. pectinata and P. zijsron (72%). Specimens were identified mostly as P. zijsron, even among Mediterranean samples and the presence of two sequence sub-clusters was highlighted in this poorly barcoded species. In conclusion, this new knowledge requires further investigations on the structure of sawfish populations and on their evolutionary dynamics to identify a suitable conservation policy.

Specifically outlining the work achieved in this PhD thesis, the work is organised into separate articles that have been published, submitted or are under preparation for submission.
Chapter 1 is an introduction, in which the state of the art and objectives are presented.
In Chapters 2-4, different potential mediators that could be used for the catalytic interaction with the enzymatic product o-AP were evaluated and due to their well characterized properties, hydrazine, NADH and ascorbic acid were selected for further study. Hydrazine is used as an antioxidant and reducing agent; NADH plays an important rule in oxidoreductases and dehydrogenase systems and ascorbic acid (vitamin C) is an antioxidant whose detection is important in clinical and food applications. The electrocatalytic properties of o-aminophenol films grafted on glassy carbon surfaces have been employed for the electrochemical evaluation of hydrazine, NADH and ascorbic acid, to select the most relevant as a recycling mediator in the planned signal amplification strategy. To evaluate the best mediator, the reaction kinetics between mediators and the o-AP/o-QI were extensively studied using different techniques such as cyclic voltammetry, hydrodynamic voltammetry, double potential step chronoamperometry, and double potential step chronocoulometry.
Of them, ascorbic acid was selected as the mediator for regeneration of the o-AP film and substrate recycling. We had thus demonstrated an interesting catalytic system for the oxidation of ascorbic acid, which is stable, sensitive and reproducible, and we decided to explore this system for clinical and food applications. In the first application, we targeted the determination of uric acid (UA) in the presence of ascorbic acid (AA), which commonly co-exist in biological fluids of humans, mainly in blood and urine (Chapter 4). In Chapters 5 and 6, the selective electrocatalytic properties of the grafted o-AP film toward ascorbic acid were also applied to its detection in real samples of fruits and vegetables using disposable one-shot screen printed electrodes. The o-AP modified screen printed electrodes showed high catalytic responses toward the electrocatalytic oxidation of ascorbic acid. The o-AP SPE sensor exhibited high sensitivity and selectivity toward ascorbic acid with excellent storage and operational stability, as well as a quantitatively reproducible analytical performance.
In the second part of the thesis, different surface engineering strategies of antibody immobilization for immunosensor construction using a linker or via direct attachment onto a Au surface using a strategy of self assembly were evaluated and compared. An alternative strategy explored was the direct anchoring of the antibody with or without a linker via the electrochemical reduction of their diazonium cations.
In Chapter 7, a comparison between these different surface chemistries methodologies for the construction of immunosensors towards the model analyte of coeliac toxic gliadin was carried out. Firstly, the self-assembled monolayer approach was evaluated based on the modification of gold surfaces with two bipodal carboxylic acid terminated thiols (thioctic acid and a benzyl alcohol disubstituted thiol, DT2). A stable SAM of DT2 was rapidly immobilized (3 h) on Au as compared with thioctic acid (100 h), although both surface chemistries resulted in highly sensitive electrochemical immunosensors for gliadin detection using an anti-gliadin antibody (CDC5), with detection limits of 11.6 and 5.5 ng/mL, respectively. The developed immunosensors were then applied to the detection of gliadin in commercial gluten-free and gluten-containing food products, showing an excellent correlation when compared to results obtained with ELISA.
In Chapter 8, another approach was explored to further improve immunosensor sensitivity and stability and furthermore to reduce the time necessary for sensor preparation was investigated looking at the direct attachment of the SATA modified full length antibody, and their F(ab) fragments onto Au electrodes. Spontaneously adsorbed SAMs of Fab-SH and CDC5-SH onto Au were rapidly formed in less than 15 minutes. The amperometric immunosensors based on Fab fragments exhibited a vastly improved detection limit as compared to the thiolated antibody with a highly sensitive response toward gliadin detection (LOD, 3.29 ng/ml for amperometric detection and 0.42 g/ml for labelless (impedimetric) detection). Moreover, the self-assembled monolayer of F(ab) fragments was extremely stable with almost no loss in response after 60 days storage at 4oC.
In Chapter 9, an alternative surface chemistry approach was explored for the modification of Au electrodes via electrochemical and spontaneous reduction of diazonium cations of a conjugate prepared from the monoclonal full length anti-gliadin antibody (CDC5) and the linker 3,5-bis(aminophenoxy)benzoic acid (DAPBA). Cylic voltammetry was chosen for surface modification via applying three potential cycles, but it was observed that an extensive washing process was necessary after each potential cycle to remove the non-specifically adsorbed molecules or formed multilayers. The affinity of the immobilized antibody toward gliadin was studied using EIS and amperometry. The modified CDC5-DAPBA surface showed a reasonable amperometric response after incubation with 5 g/ml gliadin, and exhibited excellent specificity with no response observed in the absence of the analyte.
In Chapter 10, general conclusions and future work are presented.
From the different surface chemistry strategies evaluated in this work we can conclude that the best approach is the immunosensor based on the spontaneous adsorption of thiolated F(ab) fragments on gold. This surface is easy and fast to prepare, very stable and sensitive and can be stored for long times in the appropriate conditions without lost of affinity. A good alternative to this approach seems to be the electrodeposition of antibody-diazonium conjugates, although further work is needed in order to optimize this system.
Overall, this work has contributed significantly to the vision we have for an immunosensor that avoids washes and reagent addition, where we have selected an excellent mediator for co-encapsulation with alkaline phosphatase enzymes within liposome reporter molecules, for regeneration of surface immobilised substrate following enzymatic dephosporylation, facilitating substrate recycling and increase in sensitivity and reduction in detection limit. Furthermore, we have selected an optimum surface chemistry for co-immobilisation of capture antibody molecules and enzyme substrate via the formation of self-assembled monolayers of antibody fragments on gold surfaces. Future work will focus on combining the selected mediator and surface chemistry into a sandwich immunosensor with a target sensitive liposome reporter molecule, to demonstrate a reagentless, washless ultrasesensitive immunosensing platform.
El trabajo descrito en la presente tesis ha sido organizado en capitulos en los que se detallan diferentes artículos publicados, enviados para su publicación o en preparacion en los cuales esta basada la tesis.
El Capitulo 1 es una introducción en la que se presenta el estado del arte del tema y los objetivos de la tesis.
En los Capítulos 2 a 4 se evalúan las propiedades electrocatalíticas de diferentes mediadores (hidracina, NADH y ácido ascórbico) que podrían ser utilizados en reacciones de reciclado de substratos enzimáticos en estrategias de amplificación de señal en biosensores. La hidracina es usada como antioxidante y agente reductor, el NADH es fundamental para el funcionamiento de oxidorreductasas y deshidrogenasas y el ácido ascórbico (AA, vitamina C) es de gran importancia como antioxidante. Las propiedades electrocatalíticas de monocapas de o-aminofenol (o-AP) en superficies de carbón vítreo fueron empleadas en la caracterización electroquímica de estos mediadores con el objetivo de seleccionar el mediador más adecuado. Para ello se determinaron diferentes parámetros cinéticos asociados empleando voltametría cíclica e hidrodinámica, así como cronoamperometría y cronocoulometría de doble potencial, siendo el acido ascórbico es mas adecuado en términos de coste, respuesta electroquímica y estabilidad.
Teniendo en cuenta estas propiedades del AA, se decidió explorar otras posibles aplicaciones clínicas y en análisis de alimentos de este sistema. En primer lugar se estudio la determinación de acido úrico en presencia de AA, el cual coexiste en diferentes fluidos biológicos y se estudió su determinación en muestras reales de orina (Capítulo 4).
En los Capítulos 5 y 6 se detalla la utilización de electrodos desechables modificados con o-AP fabricados con la técnica de screen-printing en la determinación de AA de ácido ascórbico en una amplia variedad de frutas y vegetales frescos y zumos comerciales. La selectividad, reproducibilidad y estabilidad de estos electrodos fueron también estudiadas.
En la segunda parte de la tesis se evalúan diferentes estrategias para la inmovilización de anticuerpos para la construcción de inmunosensores. Estas estrategias consisten en la deposición de los anticuerpos en superficies de oro mediante autoensamblaje de compuestos tiolados o la electrodeposición de sales de diazonio.
En el Capítulo 7 se compara el uso de dos compuestos ditiolados para la modificación de superficies de oro. Estos compuestos se emplearon para la inmovilización de anticuerpos en la construcción de un inmunosensor electroquímico para la detección de gliadina en muestras reales.
El Capítulo 8 es la continuación del trabajo anterior y está basado en la adsorción espontánea de fragmentos de anticuerpos o anticuerpos tiolados en superficies de Au para la detección de gliadina. Para ello se compararon las respuestas amperométricas de ambos sistemas, observándose una excelente sensibilidad en el caso de los fragmentos de anticuerpos, asi como una mayor estabilidad (hasta 60 dias a 4ºC) de este sistema.
En el Capítulo 9, se estudia una alternativa consistente en la electrodeposición de sales de diazonio conjugadas a anticuerpos. Para ello se estudiaron diferentes métodos de deposicion (electroquímicos o adsorción espontánea), siendo la deposición empleando voltametría ciclica la más adecuada. Sin embargo, esta metodología requirió de un gran número de pasos de lavado para la eliminaciñon de compuestos adsorbidos no específicamente. A pesar de esto, el anticuerpo inmovilizado mostró una buena afinidad hacia la gliadina al ser evaluada por amperometría con una excelente especificidad.
El Capítulo 10 consiste en las conclusiones generales y un plan de trabajo para el futuro.
De forma general, este trabajo ha contribuido significativamente a la culminación de una estrategia que evita pasos de lavado y de adición de reactivo en el diseño de inmunosensores. Para ello se la seleccionado el mediador más adecuado para coencapsulación con fosfatasa alcalina en liposomas para la regeneración de sustratos inmovilizados en superficies, lo cual facilita su reciclado, así como incrementa la sensibilidad y disminuye los limites de detección. Paralelamente, se han estudiado diferentes superficies para la inmovilización de anticuerpos consistentes en la deposición de los anticuerpos y sus fragmentos en superficies de oro mediante autoensamblaje de compuestos tiolados o la electrodeposición de sales de diazonio. Se propone en el futuro combinar ambas estrategias en la construcción de plataformas inmunosensoras de fácil operatividad y ultrasensibles.

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Esta pesquisa refere-se a um estudo computacional via simula??o por din?mica molecular (DM) que investiga os efeitos da temperatura na InhA, enzima 2-trans-enoil-ACP (CoA) redutase do Mycobacterium tuberculosis (MTB). A temperatura pode interferir na estrutura e fun??o prot?icas, na habilidade de liga??o de uma prote?na, na distribui??o dos microestados, na conforma??o molecular m?dia e nas rea??es enzim?ticas. A partir do in?cio do s?culo XX, os experimentos in silico tem sido cada vez mais utilizados para auxiliar na compreens?o e comprova??o das hip?teses te?ricas elaboradas em diversas ?reas da ci?ncia. Neste contexto, a simula??o por din?mica molecular (DM) tem sido uma das t?cnicas da biof?sica molecular computacional utilizadas no estudo da varia??o das propriedades estruturais do estado nativo das prote?nas e no planejamento e design de f?rmacos. Esta pesquisa investigou o efeito da temperatura sobre a enzima 2-trans-enoil-ACP (CoA) redutase (InhA) atrav?s de um estudo por simula??o pela DM (SDM). A enzima InhA ? um importante alvo para a isoniazida (INH), um dos f?rmacos utilizados no tratamento da tuberculose (TBC). O complexo enzim?tico InhA-NADH foi submetido a uma SMD a 25 ?C (298 K) e outra a 37 ?C (310 K) durante um per?odo de 20 ns. A temperatura de 37 ?C foi escolhida por corresponder ? temperatura corporal humana. Por outro lado, 25 ?C representa a temperatura ambiente utilizada nos experimentos realizados em condi??es normais de temperatura e press?o (NTP). Alguns par?metros iniciais (desvio m?dio quadr?tico, raio de giro, superf?cie acess?vel ao solvente) foram obtidos a partir da an?lise dos dados das duas trajet?rias. Existem diferen?as conformacionais estatisticamente significativas entre as estruturas 3D resultantes das SDM a 25 ?C e 37 ?C. Tamb?m pesquisou-se o efeito da temperatura sobre a flexibilidade molecular. Enquanto observamos um importante aumento da flexibilidade na regi?o de liga??o do vi substrato (al?a A, al?a B e al?a de liga??o do substrato) aos 37 ?C, as h?lices α6, α7 e α2 apresentaram Fatores-B menores na temperatura corporal humana. Na regi?o do s?tio de liga??o da coenzima, apenas tr?s res?duos (Ser20, Ile21 e Phe41) apresentaram uma menor flexibilidade com o aumento da temperatura. Pequenos aumentos de temperatura afetam significativamente a conforma??o de uma prote?na em regi?es importantes para o desempenho de suas fun??es. A eleva??o da temperatura aumenta a flexibilidade da estrutura prot?ica, por?m de forma heterog?nea, preservando regi?es que necessitam de maior estabilidade no aspecto funcional. As n?tidas modifica??es da enzima InhA e sua coenzima NADH durante um processo de altera??o de temperatura de 25 ?C para 37 ?C devem ser consideradas no decorrer do planejamento e design de qualquer f?rmaco. O conhecimento detalhado das estruturas alvo, portanto, deve levar em conta as condi??es ambientais (press?o, temperatura, pH) ?s quais ser?o submetidas em in vivo. Sugerem-se, para o futuro, pesquisas com temperaturas maiores e trabalhos com docking.

Orientador: Anete Pereira de Souza
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Com o objetivo de identificar e clonar um gene novo do DNA mitocondrial (DNAmt) de Coix lacryma-jobi L. (coix), utilizou-se a estratégia da hibridização heteróloga. Para tanto amplificou-se por PCR um fragmento correspondente a um quadro de leitura aberto ("open reading frame"-oif), denominado orf167, presente no DNAmt da briófita Marchantia polymorpha, e tido como um possível gene. Marcou-se radioativamente e utilizou-se esta sequência como sonda em hibridizações com o DNAmt de coix digerido com várias enzimas. Identificou-se um fragmento homólogo Bgl II/ Bgl II de 1,4 kb, o qual foi clonado em pBluescript. Elaborou-se o mapa de restrição deste fragmento e localizou-se nele a exata região de homologia com a orf167. A região de homologia estava presente em um fragmento interno de 0,5 kb Spe I / Pvu II. Este fragmento de 0,5 kb, homólogo à orf167, foi utilizado em hibridizações com o DNArmt de várias espécies de plantas superiores (alfafa, batata, coix, couve-flor, ervilha, milho e soja), verificando-se que o mesmo correspondia a uma seqüência altamente conservada. Este mesmo fragmento foi também hibridizado em membranas contendo o RNAmt tota de oix e de outras espécies de plantas superiores (milho e couve flor). Os resultados revelaram que ele é transcrito na mitocôndria das espécies analisadas. O fragmento original de 1,4 kb Bgl II / Bgl II foi divido em 5 subfragmentos, os quais foram clonados e sequenciados. Após a análise da homologia desta sequência com outras presentes nos bancos de dados, verificou-se que o fragmento de 1,4 kb Bgl II./ Bgl II, isolado do DNAmt de coix, contém um "cluster" gênico onde estão presentes o gene que codifica o tRNA serina (tRNAScr), um pseudo-gene provavelmente originado do tRNA fenilananina (tRNAPhe), os genes nad3 e rps12. Tais genes presentes em coix são muito similares àqueles presentes em trigo e milho, os quais se organizam também em um "c1uster" gênico muito similar ao existente em coix. Estudos de expressão realizados através de "Northern Blotting" e RT ¿PCR mostraram que os genes tRNA ser, nad3 e rps12 são transcritos, sendo os dois últimos cotranscritos. Vinte e três elones de cDNA dos transcritos dos genes nad3 e rps12 foram seqüenciados, e tiveram suas sequências comparadas com a seqüência genômica. Encontrou-se 21 sítios de edição nos transcritos do gene nad3 e 8 sítios nos transcritos do gene rps12. Após comparações entre a sequência de aminoácidos predita a partir do clone genômico e do cDNA, observou-se que todas as edições modificam o aminoácido especificado pelo codon onde O evento de edição foi detectado, tornando a sequência de aminoácidos editada diferente da prevista pela sequência genômica. Vinte sítios de edição no gene nad3, e 6 no gene rps12, alteram a identidade do codon, de modo a especificar um aminoácido mais conservado durante a evolução entre diferentes espécies vegetais. Os outros três sítios, sendo I no gene nad3 e 2 no gene rps12, acarretam mudanças raras, espécie-específicas e não conservativas. Todos os 23 elones de cDNA investigados estavam diferentemente editados, predominando os cDNAs com sítios parcialmente editados. Não foi encontrada nenhuma orientação preferencial (5' para 3', ou 3' para 5') para o processamento da edição. Discute-se os motivos do reconhecimento do gene nad3 de coix pela orf167 de M. polymorpha
Abstract: We have cloned and sequenced the nad3 and rps12 mithocondrial genes from Coix lacryma-jobi L., whose sequence were found to be similar to the corresponding genes in wheat and maize. In addition, we have indentified a tRNA Ser and a pseudo-tRNA genes on the 5¿ upstream of nad3, generating a locus organization which is identical to what has been observed in wheat and maize. The locus identification was performed with a heterologous hibridization using the mitochondrial probe orf167 from Marchantia polymorpha. The gene expression was analysed using NoI1hern hybridization and RT -PCR, indicating that nad3 and rps12 gene were cotranscribed in a 1.3 kb RNA molecule. Concernig the RNA editing, we have found 21 and 8 sites in the nad3 and rps12 genes respectively. In general terms, the observed coix mRNA editing has changed the codon identities in such a way that the NAD3- and RPS12- protein aminoacid sequence was kept closer to the corresponding ones in other organisms. However, we have detected three specie-specific editing sites which were not conservative. As for the editing processing, we have analysed 23 cDNA clones which showed different editing pattems. A predominance of partial editing was observed where the edited sites were randomly distributed.
Mestrado
Genetica Vegetal e Melhoramento
Mestre em Genética e Biologia Molecular

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A esquizofrenia ? uma doen?a neuropsiqui?trica que afeta cerca de 1% da popula??o mundial e que, devido aos seus diversos sintomas, acarreta um enorme custo social direto (hospitaliza??es, atendimentos, medica??es) e indireto (improdutividade, repercuss?es familiares). Os estudos de gen?tica populacional indicam que a esquizofrenia tenha um componente gen?tico relevante al?m da influ?ncia do ambiente. Neste sentido, al?m de estudos no DNA nuclear, t?m sido investigadas as altera??es no DNA Mitocondrial (mtDNA). O mtDNA apresenta heran?a materna, e por isso ? muito ?til em estudos populacionais. Estudos com doen?as neurodegenerativas como a doen?a de Parkinson e a doen?a de Alzheimer sugerem que, ao menos em parte, o mtDNA contribua para suas etiologias. Manifesta??es neuropsiqui?tricas caracter?sticas de encefalopatias mitocondriais causadas por muta??es do mtDNA s?o convuls?es, dem?ncia e dor de cabe?a. Al?m disso, um estado confusional agudo, com alguns sintomas semelhantes aos que ocorrem na esquizofrenia (desorganiza??o mental e alucina??es), ?s vezes ? observado em MELAS (mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes), uma encefalopatia mitocondrial t?pica. Dessa forma, o objetivo dessa pesquisa foi averiguar uma poss?vel associa??o entre polimorfismos A4769G e A10398G de mtDNA, que j? foram descritos como predisponentes a outras doen?as neuropsiqui?tricas, com o desenvolvimento da esquizofrenia. Os polimorfismos A4769G e A10398G est?o respectivamente localizados nos genes ND2 e ND3, que codificam para subunidades 2 e 3 da NADH Desidrogenase. Para relacionar esses polimorfismos com a esquizofrenia, testamos 76 pacientes esquizofr?nicos quanto ? ocorr?ncia ou n?o destas variantes polim?rficas no mtDNA e comparamos com as amostras de 88 controles sadios. Esses polimorfismos foram analisados utilizado-se o seq?enciador autom?tico de DNA MegaBACE 1000 (GE Healthcare ) do Centro de Biologia Gen?mica e Molecular da PUCRS. Os cromatogramas gerados pela corrida eletrofor?tica das rea??es de seq?enciamento foram analisadas no programa Chromas para determinar a ocorr?ncia ou n?o da varia??o polim?rfica. Quanto ? an?lise estat?stica, foi realizado teste do qui-quadrado para vari?veis categ?ricas. O n?vel de signific?ncia estat?stica foi p ≤ 0,05. Em rela??o ao polimorfismo A4769G, foram analisadas amostras de 76 pacientes dos quais 61 (80,3%) apresentaram o alelo G e 15 (19,7%) apresentaram o alelo A nesta posi??o. Das 88 amostras de controles analisadas, obtivemos 82 (93,2%) com o alelo G e 6 (6,8%) com o alelo A (Qui-quadrado p=0,014, Odds ratio=2.895). Em rela??o ao polimorfismo A10398G, dos 62 pacientes analisados, 17 (27,4%) apresentaram o alelo G e 45 (72,6%) o alelo A. Dos 76 controles, 34 (44,7%) apresentaram a presen?a do alelo mutante G e 42 (55,3%) apresentaram o alelo A para esta posi??o (Qui-quadrado p=0,036, Odds ratio=1.313). O estudo mostra diferen?as estatisticamente significativas na freq??ncia dos sistemas polim?rficos estudados entre pacientes esquizofr?nicos e controles. Estudos adicionais s?o necess?rios para avaliar sua relev?ncia do ponto de vista funcional.

Resumo: A apocinina, um métoxi-catecol (MC) extraído das raízes da planta Picrorhiza kurroa, é um eficiente inibidor do complexo NADPH oxidase (NOX) e seu mecanismo de ação está relacionado à inibição da agregação dos componentes enzimáticos e à oxidação catalisada por peroxidases. Estudamos a relação estrutura-atividade da apocinina e de metóxi-catecóis correlatos, na inibição da NOX. Com a função de alterar o potencial de redução das moléculas estudadas, escolhemos MC com grupos adicionais aceptores (MC-A) ou doadores de elétrons (MC-D) na posição para, em relação à hidroxila da molécula de apocinina. Os MC-D inibiram mais fracamente a ativação da NOX em neutrófilos ativados quando comparados aos MC-A. Acreditamos que isso se deva à fraca reatividade destes compostos com grupamentos sulfidrila de proteínas, assim, os MC-D são incapazes de oxidar grupos essenciais aos componentes citosólicos da enzima e desta forma, inibir sua ativação. A diapocinina, metabólito gerado após a oxidação da apocinina por peroxidases, foi sintetizada e avaliamos seus efeitos em neutrófilos e leucócitos mononucleares ativados quanto à inibição da ativação da NOX e em leucócitos mononucleares, em relação à liberação de citocinas e expressão do RNAm do componente de membrana gp91phox. Encontramos que a apocinina e a diapocinina inibiram os três fenômenos estudados, embora a diapocinina o tenha feito de modo mais eficiente. Acreditamos que isto possa estar relacionado ao efeito supressor da apocinina e diapocinina sobre a ativação da NADPH oxidase
Abstract: Apocynin, a methoxy catechol (MC) extracted from the roots of Picrorhiza kurroa has been used as an efficient inhibitor of the NADPH oxidase (NOX) complex and its mechanism of action involves the impairment of the assemble process of the enzyme. Here, we studied the structure-activity relationship for apocynin and analogous ortho-methoxy-substituted catechols as inhibitors of the NADPH oxidase. Aiming to alter the reduction potential, the ortho-methoxy-catechol moiety was kept constant and the substituents at para position related to the hydroxyl group were varied. Two series of compounds were employed: methoxy-catechols bearing electron-withdrawing groups (MC-W) and methoxy-catechol bearing electron-donating groups (MC-D). We found that MC-D were weaker inhibitors of the NOX complex in stimulated neutrophils compared to MD-W. We suggest that there is a close relationship between the weak reactivity of MC-D compounds with sulfhydryl residues of proteins and there incapacity in inhibiting NOX activation. Diapocynin is a product generated by peroxidase oxidation of apocynin. Here we synthesized diapocynin and compared its efficacy as NOX inhibitor in peripheral blood mononuclear cells (PBMC) and neutrophils in relation to apocynin. Both drugs were also studied in cytokine release and its influence on gp91phox mRNA expression. We found that diapocynin was a more efficient inhibitor of NOX activation, gp91phox mRNA expression and cytokine release than apocynin. We suggest that these findings could be related to NOX inhibition process
Orientador: Valdecir Farias Ximenes
Coorientador: Luiz Marcos da Fonseca
Banca: Dulce Helena Siqueira Silva
Banca: Paulo Inácio da Costa
Banca: José Carlos Rebuglio Vellosa
Banca: Cleni Mara Marzocchi Machado
Doutor

A Doença Granulomatosa Crônica é uma imunodeficiência grave e rara, na qual os quadros infecciosos por bactérias e fungos, ocorrem predominantemente nas barreiras naturais do organismo. O defeito reside em mutações em um dos componentes do sistema NADPH oxidase. O dHPLC mostrou-se mais sensível que o SSCP, sendo eficaz na detecção de alterações em 100% dos casos. Identificamos sete mutações diferentes no gene CYBB, sendo quatro delas inéditas. São elas R226X; R290X; e C537R. Dentre as mutações inéditas identificamos: T302fsX46; c.141 +5 G> T; C185R; e H222L. Identificamos a mutação V25fsX51 no gene NCF1 em duas pacientes. Estabelecemos uma correlação entre genótipo e fenótipo clínico baseado em manifestações clínicas relevantes na DGC, nos fornecendo dados importantes de cada manifestação clínica e um índice de gravidade clínica (IGC) para cada tipo de mutação. Os resultados contribuem para a construção de estratégias que permitam a identificação dos defeitos genético-moleculares relacionados à DGC.
Chronic granulomatous disease is a primary immunodeficiency characterized by recurrent and severe infections, affecting the body barriers. In these patients, phagocytes present a failure in the respiratory burst caused by a deficiency of the NADPH oxidase system, and a microbicidal defect. Mutations affecting one of the components of the NADPH oxidase system. The dHPLC proved to be more sensitive to the SSCP, being effective in detecting changes in 100% of cases. We found seven different mutations, four of which are original. Are they R226X; R290X; and C537R. Among the unpublished mutations identified: T302fsX46; c. 141 + 5 G > T; C185R; and H222L. We identify the gene mutation V25fsX51 NCF1 in two patients. We have established a correlation between genotype and phenotype clinical relevant clinical manifestations based on DGC in providing important data from each clinical and clinical severity index (CSI) for each type of mutation. The results contribute to the construction of strategies enabling the identification of molecular genetic defects related to CGD.