Made available in DSpace on 2014-07-29T15:30:41Z (GMT). No. of bitstreams: 1 Dissertacao Rogerio Troian.pdf: 1860424 bytes, checksum: ba62f125166320434b87b83d216fc4e4 (MD5) Previous issue date: 2009-02-26 / Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of paracoccidioidomycosis (PCM), a prevalent systemic mycosis in Latin America. Pathogenicity appears to be intimately related to the dimorphic transition from the hyphal to the yeast form, which is induced by a shift from environmental temperature to the temperature of the mammalian host. To cope with nutrient deprivation during the infection process, a number of pathogens employ the glyoxylate cycle (GC) to utilize fatty acids as carbon sources. The genes which constitute this pathway have been implicated in pathogenesis. An important aspect in the interaction between P.brasiliensis and your host is the ability to adhere to matrix extracelular components. In this work has shown that the isocitrate lyase of P. brasiliensis (PbICL) is located in the cell wall and also in the cytoplasm. PbICL recombinant and polyclonal antibody were able to inhibit the interaction of P. brasiliensis to epithelial cell cultures in vitro. Was also evaluated the ability of PbICL recombinant to connect the components of the extracellular matrix such as laminin, fibronectin, collagen type I and IV. These results suggest that PbICL is necessary to interaction between molecules of the extracellular matrix and P.brasiliensis, and that this interaction is crucial in adhesion and invasion of the fungus to the host cells. The kinetic parameters of PbICLr were determined. The sequence coding for methylisocitrate lyase of P. brasiliensis (PbmeICL) and the recombinant protein PbmeICLr were obtained. / Paracoccidioides brasiliensis, um fungo termodimórfico, é o agente causador da paracoccidioidomicose (PCM), uma micose sistêmica prevalente da América Latina. A patogenicidade aparenta estar intimamente relacionada com a transição dimórfica da fase de micélio para levedura presente no hospedeiro. Para suprir a deficiência de nutrientes durante o processo de infecção, alguns patógenos empregam o ciclo do glioxalato (CG) na utilização de ácidos graxos como fontes de carbono. Os genes que constituem esta via têm sido relacionados à patogênese. Um aspecto importante na interação entre P. brasiliensis e seu hospedeiro é a habilidade do fungo em aderir aos componentes da matriz extracelular. Nesse trabalho foi demonstrado que a isocitrato liase de P. brasiliensis (PbICL) está localizada na parede celular e também no citoplasma. PbICL recombinante (PbICLr) e o seu respectivo anticorpo policlonal foram capazes de inibir a interação de P. brasiliensis às culturas de células epiteliais in vitro. Foi avaliada também a capacidade da PbICLr de se ligar a componentes da matriz extracelular, como laminina, fibronectina, colágeno tipo I e IV. Esses resultados sugerem que PbICL é necessária para interação entre P. brasiliensis e moléculas da matriz extracelular, sendo essa interação fundamental na aderência e invasão do fungo às células do hospedeiro. Os parâmetros cinéticos da PbICLr foram determinados. A sequência que codifica para a metilisocitrato liase de P. brasiliensis (PbmeICL), bem como a proteína recombinante PbmeICLr foram obtidas.

Submitted by Helena Bejio (helena.bejio@unioeste.br) on 2017-11-23T17:51:39Z No. of bitstreams: 2 Eloisa Lorenzetti 2017.pdf: 1638897 bytes, checksum: 37d0d636adf093d3df43c201d58eeb5b (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-11-23T17:51:39Z (GMT). No. of bitstreams: 2 Eloisa Lorenzetti 2017.pdf: 1638897 bytes, checksum: 37d0d636adf093d3df43c201d58eeb5b (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-02-10 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Several works using extracts obtained from medicinal plants have demonstrated direct and potential antimicrobial action to induce the accumulation of secondary metabolites, which are very important as plant defense mechanisms against pathogens. The objective of this work was to develop an alternative method using rosemary extract (Rosmarinus officinalis L.) at concentrations 0%, 1%, 2.5% and 5%, to verify the antimicrobial activity against Macrophomina phaseolina, control of charcoal rot in soybean stem and determine the activity of peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase (PAL) and protein content on soybean plants. We performed in vitro assays in order to analyze mycelial growth of the fungus, fungus mass and number of micro-sclerotia, greenhouse tests to evaluate the area under the disease progress curve (AUDPC), and biochemical analyzes to verify a possible induction of resistance in the treated plants. For the determination of the defense enzymes, soybean plants were treated with the extracts and inoculated with M. phaseolina. Samples were collected at 0, 36, 72, 120, 168, 216 and 264 h after treatment. The rosemary extract reduced by 44% and 74% the fungal growth on solid and liquid media, respectively, while for the micro-sclerotia the reduction was of 61%. For the AUDPC in the first and in second assays, there were a reduction of 53% and 56% respectively in the disease. For the samples collected at the base of steam, peroxidase had the highest concentrations of the extract with two peaks of induction. The polyphenol oxidase activity increased from 36 to 120 hours after treatment with extract at 5%. PAL activity was induced only with 5% extract, with increases 83% and 130% higher in times 168 and 216 hours after treatment, respectively. For enzymes activities in root, peroxidase again showed two peaks for increase at 5% concentration, polyphenol oxidase was 426% higher at 216 hours after treatment and PAL showed an increase of 340% at 216 hours after treatment with 5% extract. These results indicate potential of rosemary extract in the control of charcoal rot in soybean and in the induction of plant defense enzymes in soybean. / Diversos trabalhos utilizando extratos obtidos de plantas medicinais têm demonstrado ação antimicrobiana direta e potencial de induzir o acúmulo de metabólitos secundários, sendo estes muito importantes nos principais mecanismos de defesa das plantas aos patógenos. O objetivo deste trabalho foi desenvolver um método alternativo através da utilização do extrato de alecrim (Rosmarinus officinalis L.), nas concentrações 0%, 1%, 2,5% e 5%, para verificar a atividade antimicrobiana contra Macrophomina phaseolina, controlar a podridão cinzenta da haste em soja e determinar as atividades de peroxidase, polifenoloxidase, fenilalanina amônia-liase e teor de proteína de plantas de soja tratadas. Foram realizados ensaios in vitro a fim de analisar o crescimento micelial do fungo, a massa do fungo e o número de microescleródios, ensaios in vivo em casa de vegetação para avaliar a área abaixo da curva de progresso da doença (AACPD), além de análises bioquímicas para verificar uma possível indução de resistência nas plantas tratadas. Para determinação das enzimas de defesa, plantas de soja foram tratadas com os extratos e inoculadas com M. phaseolina, sendo retiradas amostras para análise nos tempos 0, 36, 72, 120, 168, 216 e 264 h após o tratamento. O extrato de alecrim reduziu em até 44% e 74% o crescimento fúngico em meios sólido e líquido, respectivamente, enquanto que para micro-escleródios a redução foi de 61%. Para AACPD, no primeiro e no segundo ensaios houve redução de 53% e 56% respectivamente. Nas amostras retiradas do colo das plantas, para peroxidase, as concentrações mais elevadas do extrato proporcionaram dois picos de indução. Houve constante incremento na atividade de polifenoloxidase desde 36 até 120 h após o tratamento para a concentração 5% do extrato de alecrim. Para FAL apenas a concentração 5% promoveu incremento 83% e 130% maior nos tempos 168 e 216 h após o tratamento, respectivamente. Para as atividades na raiz, a peroxidase novamente apresentou dois picos de incremento para a concentração 5% do extrato, a polifenoloxidase foi 426% maior na concentração 5% às 216 h após o tratamento e a atividade de FAL apresentou incremento de 340% no tempo 216 h após o tratamento com 5% do extrato. Estes resultados indicam potencial do extrato de alecrim no controle de podridão cinzenta da haste em soja e na indução da atividade de enzimas de defesa em colo e raiz de soja.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2017-06-02T19:54:07Z No. of bitstreams: 1 2015 - Soraia John da Silva.pdf: 1762972 bytes, checksum: aae3e43996736241367a1924339662c0 (MD5) / Made available in DSpace on 2017-06-02T19:54:07Z (GMT). No. of bitstreams: 1 2015 - Soraia John da Silva.pdf: 1762972 bytes, checksum: aae3e43996736241367a1924339662c0 (MD5) Previous issue date: 2015-08-20 / CAPES / The glyphosate, herbicide used in different countries, inhibits the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), blocking the synthesis of aromatic amino acids. With this, it still affects the activity of phenylalanine ammonia lyase (PAL) and the concentration of metabolites in plants. Its activity was first reported as a metal chelator. Therefore, to make use of this herbicide, may be formation of complexes with metals from soil, occurring change in the effectiveness of the product and loss of minerals. Thus, to avoid such problems,this study aimed to compare the effectiveness of three forms of glyphosate: purified, previously complexed with metals, and a commercial form (Roundup WG?). The effects of glyphosate complexes with copper, cobalt and nickel with different stoichiometries and different pH values on the in vitro activity of EPSPs were evaluated. Selected complex for the first experiment in vivo were Cu421 and Co821 (first number for pH and the latter two to stoichiometry glyphosate: metal). These complexes were used in the in vivo experiment I, as well as distilled water (control), purified Roundup and glyphosate on transgenic soybean and B. decumbens. In the following experiments (II and III), mineral oil was used in all treatments to reduce leaching of the compounds. The complex selected for continuation of this study was Cu421 due to its emphasis on the results obtained in the first experiment in vivo. When comparing the effect of the compounds in Falker Chlorophyll Index (ICF) of B. decumbens compared to control, there was fall of this index when using Roundup, Cu421 and purified glyphosate (the latter only in the second experiment). Later it was analyzed fresh mass accumulation and collected fresh material for determination of enzyme activities and N-NO3- levels. The complex Cu421 caused a more significant fresh mass reduction and still allowed the increase in the content of soluble nitrate in Brachiaria decumbens, probably due to the presence of nitrate in this complex. In the case of transgenic soybean there was no significant change in ICF. The use of Roundup and the complex did not change significantly the fresh mass accumul ation in this species. The application of the purified glyphosate, however, caused increase in mass accumulation and all treatments altered soybeans in nitrate content. In experiments with mineral oil in B. decumbens, the Cu421 complex inhibited significantly the EPSPs activity, as well as purified Roundup and glyphosate (the latter only in the experiment III). No inhibition occurred in transgenic soybean. All treatments in vivo stimulated PAL activity only on weed, which suggests that the increase in this activity is a consequence of the inhibition of EPSPs and other deleterious effects of compounds on susceptible plants. This study showed that especially Cu421 complex might be used effectively as a herbicide since it inhibits EPSPs, activates the PA,L reduces fresh mass accumulation and influences photosynthesis in the tested weed. Besides, the transgenic soybean showed little sensitive to this compound, which further increases the prospect of using the same as herbicide. / O glifosato, herbicida usado mundialmente, atua inibindo a enzima 5-enolpiruvil-chiquimato- 3-fosfato-sintase (EPSPs), bloqueando a s?ntese de amino?cidos arom?ticos. Com isso, ainda influencia a atividade de fenilalanina am?nia liase (PAL) e a concentra??o de metab?litos nas plantas. A sua primeira a??o reportada foi como agente quelante de metais. Portanto, ao fazer uso deste herbicida, pode haver forma??o de complexos com metais do solo, ocorrendo altera??o da efic?cia do produto e defici?ncia mineral. Assim, de modo a evitar tais problemas, este trabalho teve como objetivo, comparar a efici?ncia de tr?s formas de glifosato: purificado, previamente complexado com metais, e uma das suas formas comerciais (Roundup WG?). Os efeitos de complexos de glifosato com cobre, cobalto e n?quel, sintetizados sob diferentes estequiometrias e valores de pH, foram avaliados sobre a atividade in vitro de EPSPs. Os complexos selecionados para o primeiro experimento in vivo foram: Cu421 e Co821 (primeiro n?mero referente ao pH e os dois ?ltimos ? estequiometria glifosato:metal). Estes complexos foram usados no experimento in vivo I, assim como ?gua destilada (controle), Roundup e glifosato purificado, sobre soja transg?nica e Brachiaria decumbens. Nos experimentos seguintes utilizou-se ?leo mineral em todos os tratamentos para reduzir a lixivia??o dos compostos. O complexo selecionado para continua??o deste estudo foi o Cu421 devido a seu destaque nos resultados obtidos no primeiro experimento in vivo. Ao comparar o efeito dos compostos no ?ndice de Clorofila Falker (ICF) de B. decumbens em rela??o ao controle, observou-se queda deste ?ndice ao usar Roundup, Cu421 e glifosato purificado (este ?ltimo, somente no segundo experimento). Posteriormente foi analisado ac?mulo de massa fresca e coletado material fresco para determina??o das atividades enzim?ticas e dos teores N-NO3-. O complexo Cu421 foi o que provocou maior redu??o da massa fresca e ainda possibilitou o aumento no teor sol?vel de nitrato em B. decumbens, provavelmente devido ? presen?a de nitrato neste complexo. No caso da soja transg?nica n?o houve altera??o significativa de ICF. O uso de Roundup e dos complexos n?o alterou de forma significativa o ac?mulo de massa fresca nesta esp?cie. A aplica??o do glifosato purificado, entretanto, causou incremento no ac?mulo de massa e todos os tratamentos alteraram o teor de nitrato em soja. Nos experimentos com ?leo mineral em B. decumbens, o complexo Cu421 inibiu de forma significativa a atividade de EPSPs, assim como Roundup e glifosato purificado (este ?ltimo, somente no experimento III). Em soja transg?nica n?o houve inibi??o. Todos os tratamentos in vivo estimularam a atividade de PAL somente na gram?nea, permitindo sugerir que o aumento nesta atividade seja consequ?ncia da inibi??o de EPSPs e de outros efeitos delet?rios dos compostos sobre plantas suscept?veis. O presente estudo mostrou que principalmente o complexo Cu421 pode vir a ser utilizado de forma eficaz como herbicida, uma vez que inibe a EPSPs, ativa a PAL, reduz ac?mulo de massa fresca e influencia a fotoss?ntese na planta daninha testada. E, em contrapartida, a soja transg?nica mostrou-se pouco sens?vel a este composto, o que aumenta ainda mais a perspectiva do uso do mesmo como herbicida.

Organoarsenicals such as methylarsenical methylarsenate (MAs(V)) and aromatic arsenicals including roxarsone (4-hydroxy-3-nitrophenylarsenate or Rox(V)) have been extensively used as an herbicide and growth enhancers in animal husbandry, respectively. They undergo environmental degradation to more toxic inorganic arsenite (As(III)) that contaminates crops and drinking water. We previously identified a bacterial gene (arsI) responsible for aerobic MAs(III) demethylation. The gene product, ArsI, is a Fe(II)-dependent extradiol dioxygenase that cleaves the carbon-arsenic (C-As) bond in MAs(III) and trivalent aromatic arsenicals. The objective of this study was to elucidate the ArsI mechanism. Using isothermal titration calorimetry, we determined the dissociation constants (Kd) and ligand-to-protein stoichiometries (N) of ArsI for Fe(II), MAs(III) and aromatic phenyl arsenite. Using a combination of methods including chemical modification, site-directed mutagenesis, and fluorescent spectroscopy, we demonstrated that amino acid residues predicted to participate in Fe(II)-binding (His5-His62-Glu115) and substrate binding (Cys96-Cys97) are all involved in catalysis. Finally, the products of Rox(III) degradation were identified as As(III) and 4-hydroxy-2-nitrophenol, demonstrating that ArsI is a dioxygenase that incorporates one oxygen atom from dioxygen into the carbon and the other to the arsenic to catalyze the cleavage of the C-As bond. These results augment our understanding of the mechanism of this novel C-As lyase.

Eine der für die biotechnologische Nutzung interessanten Eigenschaften der Hefe Yarrowia (Y.) lipolytica ist ihr Vermögen, unter bestimmten Kultivierungsbedingungen große Mengen an organischen Säuren, darunter auch Citronensäure (CS), ins extrazelluläre Medium zu sekretieren. Aufgrund ihrer Apathogenität, ihres breiten Substratspektrums und ihrer guten molekulargenetischen und verfahrenstechnischen Handhabbarkeit, stellt sie einen idealen Mikroorganismus zur biotechnologischen Gewinnung von Citronensäure dar. Bei der durch eine Stickstofflimitation ausgelösten Überproduktion von CS mit Y. lipolytica kommt es parallel auch zur Ausscheidung von Isocitronensäure (ICS), deren Anteil am Gesamtsäureprodukt in Abhängigkeit von der C-Quelle in Wildtypstämmen zwischen 10 % (Glucose, Saccharose, Glycerol) und 40-55 % (Pflanzenöle, Alkan) liegt. In der Literatur beschriebene Mutantenstämme von Y. lipolytica besitzen ein von Wildtypstämmen abweichendes Produktmuster und können sowohl weniger (2-5 % auf Glucose, 5-10 % Alkan und Pflanzenöl) als auch mehr ICS (15-35 % Glu¬cose, 65-75 % Alkan, Ethanol bzw. Pflanzenöl) sekretieren. Die gezielte Überexpression des für die Isocitratlyase codierenden Gens ICL1 durch die Erhöhung der Kopiezahl führte zu einer drastischen Erhöhung der Enzymaktivität in den entsprechenden ICL1 multicopy Transformanden (10-15fach gegenüber Wildtyp) aufgrund des Gen-Dosis-Effektes. Auf den getesteten hydrophilen C-Quellen Glucose, Glycerol und Saccharose verringerte sich der ICS-Anteil von durchschnittlich 10-12 % auf 3-5 %, auf den hydrophoben C-Quellen Hexadecan und Sonnenblumenöl sogar von durchschnittlich 40-55 % auf Werte um 5-10 %. Im Ergebnis dieser Untersuchungen entstand ein Patent (DE10333144A1), welches ein Verfahren zur Gewinnung von CS mit einer genetisch veränderten Hefe Y. lipolytica beschreibt. Die Zerstörung des Leserahmens des ICL1 Gens in Mutantenstämmen bewirkte das Ausbleiben der Synthese einer funktionell aktiven Isocitratlyase, was den Verlust der Fähigkeit zur Verwertung gluconeogenetischer C-Quellen wie Ethanol, Alkan und Pflanzenölen zur Folge hatte. Auf Glucose bzw. Glycerol zeigten diese Mutantenstämme im Vergleich zum Wildtypstamm jedoch nur eine geringe Erhöhung des ICS-Anteils um durchschnittlich 2-5 Prozentpunkte. Die Zerstörung des Leserahmens des IDP2 Gens, codierend für die NADP-abhängigen Isocitratdehydrogenase, führte zur Glutamat-Auxotrophie des entsprechenden Mutantenstammes auf allen getesteten C-Quellen. In der Produktbildung zeigte diese Mutante im Vergleich zum Wildtypstamm eine Verringerung des ICS-Anteils um durchschnittlich 2-4 Prozentpunkte. Es konnte gezeigt werden, dass Saccharose ein geeignetes Substrat zur Gewinnung von CS mit rekombinanten Stämmen von Y. lipolytica darstellt, die das für die Invertase codierende SUC2 Gens aus Saccharomyces cerevisiae exprimieren. Natürlicherweise kann Y. lipolytica diesen Zucker aufgrund des Fehlens des Enzyms Invertase nicht verwerten. Im Schüttelkolben wurden aus 100 g/l Saccharose unter nicht optimierten Bedingungen bereits 56 g/l CS+ICS gewonnen. Nach der Optimierung durch die Reduktion des für die Invertaseexpression durch pXPR2 notwendigen Peptonanteils von 1,7 auf 0,4 g/l erhöhte sich die Produktkonzentration auf 77 g/l. Die Übertragung des Produktionsprozesses in den Bioreaktor hatte die Verdopplung der Produktbildungsraten (RZA von 0,4 auf 0,85 g/l*h, r von 46 auf 89 mg/g*h) zur Folge, bedingt durch die Aufhebung der Sauerstofflimitation. Die Steigerung der Invertaseaktivität, die sich unter Bioreaktorbedingungen als ein Limi¬tationsfaktor her¬ausstellte, konnte durch die Anhebung des pH-Wertes von 5,0 auf 6,0 bzw. 6,8 er¬reicht werden. Dadurch konnten die Produktbildungsrate RZA um bis zu 80 % von 0,42 auf 0,76 g/l*h, die biomassespezifische Produktbildungsge¬schwin¬digkeit r um bis zu 70 % von 0,06 auf 0,1 g/g*h und die Ausbeute um bis zu 64 % von 0,5 auf 0,82 g/g gesteigert werden. Einen weiteren Limitationsfaktor für den CS-Bildungsprozess aus Saccharose stellt bei ausreichender Invertaseexpression offenbar die Aufnahme von Glucose und Fructose dar. Die Hefe Y. lipolytica zeigte höchste Produktbildungsraten aus Pflanzenölen, wie Sonnenblumen- oder Rapsöl, als nachwachsende Rohstoffe. Um zu prüfen, ob die Produktivität der CS-Bildung aus Pflanzenölen mit Y. lipolytica gesteigert werden kann, sollte die Triglyceridverwertung durch die Erhöhung der extrazellulären Lipaseaktivität verbessert werden. Dazu wurden zum einen Insertionsmutantenstämme, die auf eine erhöhte extrazelluläre Lipaseaktivität im Plattentest hin selektiert wurden, charakterisiert. Zum anderen wurde das für die extrazelluläre Lipase codierende LIP2 Gen in Y. lipolytica überexprimiert. Die erhaltenen LIP2 multicopy Transformanden zeigten eine bis zu 400fach erhöhte Lipaseaktivität im Vergleich zum Wildtypstamm (von 400 U/l auf bis zu 150000 U/l). Eine Verbesserung der Triglyceridverwertung aufgrund der Erhöhung der extrazellulären Lipaseaktivität in den untersuchten Insertionsmutanten und LIP2 multicopy Transformanden wurde nicht festgestellt. Die erhaltenen Daten für die Produktbildungsrate RZA (0,9-1,1 g/l*h), die biomassespezifische Produktbildungsgeschwindigkeit r (0,08-0,14 g/g*h) und die Ausbeuten (1,3-1,5 g/g) waren innerhalb der untersuchten Stämme vergleichbar und ließen keine verbesserte Produktbildung erkennen. Der geschwindigkeitsbestimmende Schritt liegt offenbar nicht bei der Hydrolyse der Triglyceride durch Lipasen, sondern bei der Aufnahme und dem Transport der Fettsäuren und/oder deren Katabolismus.

<p>Bacterial endospores have been a topic of research interest over the last several decades given their high resistance to ultraviolet (UV) damage. Unlike vegetative bacterial cells, which form cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) as the major product upon UV irradiation, endospore bacteria form a spore photoproduct (5-(<em>R</em>-thyminyl)-5,6-dihydrothymine or SP) as the major product. Vegetative bacteria cells are subject to regular cell activities and processes such as division and deoxyribonucleic acid (DNA) replication, which are prone to damage from UV exposure. However, in endospores, which have a largely anhydrous inner environment, the DNA remains dormant when bound to spore-specific small acid-soluble proteins (SASP) and dipicolinic acid, making spores highly resistant to radiation, heat, desiccation, and chemical harm. During spore germination, SP lesions in DNA are repaired by a distinctive repair enzyme, spore photoproduct lyase (SPL). In this thesis, molecular dynamics (MD) simulations were carried out to (i) examine how the formation of the SP lesion in DNA affects the global and local structural properties of duplex DNA and (ii) study how this lesion is recognized and repaired in endospore. The first part of this work was focused on designing and developing a structurally and dynamically stable model for dinucleotide SP molecule (TpT), which was subsequently used as an SP patch incorporated into duplex DNA. Computationally, this requires modifications of the bond and nonbonded force field parameters. The stability of the patch and developed parameters was tested via solution-phase MD simulations for the SP lesion incorporated within the B-DNA dodecamer duplex (PDB 463B). The second part involved applying the new SP patch to simulate the crystallographic structure of the DNA oligomer containing SP lesions. Solution-phase MD simulations were performed for the SP-containing DNA oligomers (modeled based on PDB 4M94) and compared to the simulations of the native structure (PDB 4M95). Our analysis of the MD trajectories revealed a range of SP-induced structural and dynamical changes, including the weakened hydrogen bonds at the SP sites, increased DNA bending, and distinct conformational stability and distribution. In the third part of this thesis project, we carried out MD simulations of SP-containing DNA bound with SASPs to examine how the DNA interacts differently with SASP in the presence and absence of the SP lesion. The simulation results suggested decreased electrostatic and hydrogen bonding interactions between SASP and the damaged DNA at the SP site compared to the undamaged DNA-protein complex. In addition, decreased helicity percentage was observed in the SASPs that directly interact with the SP lesion. The last part of this this thesis work focused on the SP-dimer flipping mechanism, as the lesion is likely flipped out to its extrahelical state to be recognized and repaired by SPL. Using steered molecular dynamic (SMD) simulations and a pseudo-dihedral angle reaction coordinate, we obtained possible SP flipping pathways both in the presence and absence of SASP. Collectively, these simulation results lend new perspectives toward understanding the unique behavior of the SP lesion within the DNA duplex and the nucleoprotein complex. They also provide new insights into how the SP lesion is efficiently recognized and repaired during spore germination.</p>

L’une des particularités fondamentales caractérisant les cellules végétales des cellules animales est la présence de la paroi cellulaire entourant le protoplaste. La paroi cellulaire joue un rôle primordial dans (1) la protection du protoplaste, (2) est impliquée dans les mécanismes de filtration et (3) est le lieu de maintes réactions biochimiques nécessaires à la régulation du métabolisme et des propriétés mécaniques de la cellule. Les propriétés locales d’élasticité, d’extensibilité, de plasticité et de dureté des composants pariétaux déterminent la géométrie et la forme des cellules lors des processus de différentiation et de morphogenèse. Le but de ma thèse est de comprendre les rôles que jouent les différents composants pariétaux dans le modelage de la géométrie et le contrôle de la croissance des cellules végétales. Pour atteindre cet objectif, le modèle cellulaire sur lequel je me suis basé est le tube pollinique ou gamétophyte mâle. Le tube pollinique est une protubérance cellulaire qui se forme à partir du grain de pollen à la suite de son contact avec le stigmate. Sa fonction est la livraison des cellules spermatiques à l’ovaire pour effectuer la double fécondation. Le tube pollinique est une cellule à croissance apicale, caractérisée par la simple composition de sa paroi et par sa vitesse de croissance qui est la plus rapide du règne végétal. Ces propriétés uniques font du tube pollinique le modèle idéal pour l’étude des effets à courts termes du stress sur la croissance et le métabolisme cellulaire ainsi que sur les propriétés mécaniques de la paroi. La paroi du tube pollinique est composée de trois composantes polysaccharidiques : pectines, cellulose et callose et d’une multitude de protéines. Pour comprendre les effets que jouent ces différents composants dans la régulation de la croissance du tube pollinique, j’ai étudié les effets de mutations, de traitements enzymatiques, de l’hyper-gravité et de la gravité omni-directionnelle sur la paroi du tube pollinique. En utilisant des méthodes de modélisation mathématiques combinées à de la biologie moléculaire et de la microscopie à fluorescence et électronique à haute résolution, j’ai montré que (1) la régulation de la chimie des pectines est primordiale pour le contrôle du taux de croissance et de la forme du tube et que (2) la cellulose détermine le diamètre du tube pollinique en partie sub-apicale. De plus, j’ai examiné le rôle d’un groupe d’enzymes digestives de pectines exprimées durant le développement du tube pollinique : les pectate lyases. J’ai montré que ces enzymes sont requises lors de l’initiation de la germination du pollen. J’ai notamment directement prouvé que les pectate lyases sont sécrétées par le tube pollinique dans le but de faciliter sa pénétration au travers du style. / One of the most important features characterizing plant cells and differentiating them from animal cells is the cell wall that surrounds them. The cell wall plays a critical role in providing protection to the protoplast; it acts as a filtering mechanism and is the location of many biochemical reactions implicated in the regulation of the cell metabolism and the mechanical properties of the cell. The local stiffness, extensibility, plasticity and elasticity of the different cell wall components determine the shape and geometry of the cell during differentiation and morphogenesis. The goal of my thesis is to understand the role played by the different cell wall components in shaping the plant cell and controlling its growth behaviour. To achieve this goal, I studied the pollen tube, or male gametophyte, as a cellular model system. The pollen tube is a cellular protuberance formed by the pollen grain upon its contact with the stigma. Its main purpose is to deliver the sperm cells to the female gametophyte to ensure double fertilization. The pollen tube is a tip-growing cell characterized by its simple cell wall composition and by the fact that it is the fastest growing cell of the plant kingdom. This makes it the ideal model to study the effects of drugs, mutations or stresses on cellular growth behaviour, metabolism and cell wall mechanics. The pollen tube cell wall consists mainly of proteins and three major polysaccharidic components: pectins, cellulose and callose. To understand the role played by these components in regulating pollen tube growth, I investigated the effects of mutations, enzymatic treatments, hyper-gravity and omni-directional gravity on the pollen tube cell wall. Using mathematical modeling combined with molecular biology and high-resolution electron and fluorescent microscopy I was able to show that the regulation of pectin chemistry is required for the regulation of the growth rate and pollen tube shape and that cellulose is crucial for determining the pollen tube diameter in the sup-apical region. Moreover, I investigated the role of the pectate lyases, a group of pectin digesting enzymes expressed during pollen tube development, and I showed that this enzyme activity is required for the initiation of pollen germination. More importantly, I directly showed for the first time that the pollen tube secretes cell wall loosening enzymes to facilitate its penetration through the style.

Reported in this dissertation are the results of investigations performed at the New Orleans Center for Mass Spectrometry at the University of New Orleans. The projects that are detailed in the coming pages take on a variety of subjects, but a common thread is that each employs matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to solve a problem. Fundamental aspects of MALDI in-plume ionization are implicated in the introduction of a newly developed electron-transfer secondary ionization matrix. The remaining projects are related to the ever expanding field of proteomics. Mass spectrometry was used to investigate the site specificity of a newly developed bilin-lyase enzyme, a new approach was developed to distinguish between A-ring and D-ring attachment of bilins, and F. grandis protein expression pattern was investigated in several tissues. All obtained results were acquired using a MALDI TOF/TOF mass spectrometer. The sensitivity, mass accuracy, mass resolution and the ability to perform collision induced decomposition (CID) experiments were all valuable features that served to raise the quality of data, and thereby improved the detail of inferences to be drawn for the different projects.

Made available in DSpace on 2017-07-10T17:37:10Z (GMT). No. of bitstreams: 1 Sarah_Romano_Ortolan.pdf: 975526 bytes, checksum: d72ab61fc7bdc88b6ddbab0eb3a86e42 (MD5) Previous issue date: 2015-07-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Wheat is considered the main cereal diet of the world population, but in recent years has achieved some gain in productivity of this culture despite having increased the use of nitrogen fertilizer. The use of plant growth promoting bacteria such as Herbaspirillum seropedicae SmR1 among others has been studied to obtain development of plants with less use of nitrogen fertilizers. However there is little information relating the effects of this interaction in plant development and grain yield. Objective of this study was to evaluate the carbon and nitrogen metabolism by certain enzymes, metabolites and indices related to the response to infectious stress on the wheat cultivars CD 104 and CD 120 in association with Herbaspirillum seropedicae bacteria. Two experiments were conducted. The experimental design was completely randomized with four replications in a 4x2. The first factor relates to the conditions inoculation with bacteria and/or nitrogen source in coverage are: control without inoculation with bacteria or added nitrogen fertilizer (C); application of nitrogen fertilizer (50 kg.ha-1) 30 days after sowing (N); inoculation with 106 cells of the bacterium H. seropedicae/seed at planting (Hs) and inoculation with bacteria combined with the application of nitrogen fertilizer (Hs + N) and the second factor refers to the phenological stages (tillering and booting). The results indicated that inoculation with H. seropedicae in wheat seeds of cv.s CD 104 and CD 120 in the two growth stages answered in relation to the indices related to stress with the involvement of enzymes of carbon and nitrogen metabolism. However prominent effect was not noticed to promote plant growth of wheat in late development, nor a deleterious effect of the bacterium for inoculation cv. CD 104 under the experimental conditions. For cv. CD 120 the differential effects indicate lower levels of stress and some level of association to positive effect on productivity when combined inoculation of bacteria to nitrogen fertilization. It was concluded that as well as pathogenic and stressors, H. seropedicae able to beneficially associate with wheat also provides similar interference pattern of carbon and nitrogen metabolism and stress levels / O trigo é considerado o principal cereal da dieta da população mundial, entretanto nos últimos anos tem se obtido pouco ganho de produtividade desta cultura apesar de se ter aumentado o uso de fertilizante nitrogenado. O uso de bactérias promotoras do crescimento vegetal, como Herbaspirillum seropedicae SmR1 entre outras, tem sido estudado para se obter desenvolvimento de plantas com menor uso de fertilizantes nitrogenados. Entretanto existem poucas informações que relacionam os efeitos desta interação no desenvolvimento da planta e de produtividade de grãos. Objetivo deste trabalho foi avaliar o metabolismo de carbono e nitrogênio através de algumas enzimas, metabólitos e índices relacionados à resposta ao estresse infeccioso em trigo das cultivares CD 104 e CD 120 em associação com a bactéria Herbaspirillum seropedicae em dois estádios fenológicos. Foram realizados dois experimentos. O delineamento experimental utilizado foi o inteiramente ao acaso, com 4 repetições, em esquema fatorial 4x2. O primeiro fator refere-se às condições de inoculação com bactéria e/ou fertilização nitrogenada em cobertura, sendo: controle, sem inoculação com bactéria ou adição de fertilizante nitrogenado (C); aplicação de fertilizante nitrogenado (50 kg.ha-1) após 30 dias da semeadura (N); inoculação de 106 células da bactéria H. seropedicae/semente na semeadura (Hs) e inoculação com a bactéria combinada com a aplicação de fertilizante nitrogenado (Hs + N) e o segundo fator refere-se aos estádios fenológicos (perfilhamento e emborrachamento). Os resultados indicaram que a inoculação com H. seropedicae em sementes de trigo das cv.s CD 104 e CD 120 nos dois estádios fenológicos responderam em relação aos índices relacionados ao estresse com envolvimento das enzimas do metabolismo de carbono e nitrogênio. Entretanto não foi percebido efeito proeminente de promoção do crescimento vegetal no final do desenvolvimento do trigo, tampouco efeito deletério da inoculação de bactéria para a cv. CD 104, nas condições experimentais. Para a cv. CD 120 os efeitos diferenciais indicam menor nível de estresse e algum nível de associação para efeito positivo na produtividade quando combinada a inoculação da bactéria com a fertilização nitrogenada. Foi possível concluir que assim como para agentes patogênicos e estressantes, a H. seropedicae, capaz de associar beneficamente com trigo também apresenta padrão semelhante de interferência do metabolismo de carbono e nitrogênio e índices de estresse

Work presented in this thesis is in two parts. Part one: The X-ray crystal structures of potential antimicrobial drug targets. The protein IspF (2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, EC: 4.6.1.12) from two pathogens (Burkholderia cenocepacia and Plasmodium falciparum) has been investigated. IspF is an enzyme of isoprenoid-precursor biosynthesis and is considered to be a potential drug target. The results of structural and fragment-screening efforts presented here inform early stage drug discovery efforts. The structure of the PabC protein (4-amino-4-deoxychorismate lyase, EC: 4.1.3.38) from the Gram-negative pathogen Pseudomonas aeruginosa was also determined. PabC is involved in the production of para-aminobenzoic acid on the path to folate. Comparisons with previously solved PabC structures identified a spatially conserved tyrosine residue in the active site and suggest that a re-evaluation of a published mechanism is warranted. Part two: Immunity proteins in the Gram-negative Type VI secretion system. The X-ray crystal structures of the proteins Rap1a and Rap2a from Serratia marcescens, inhibitors of the peptidoglycan amidase toxins secreted by some Gram-negative bacteria employing the Type VI secretion pathway, were determined by molecular replacement and analysed.