Structure and lipid interactions of membrane-associated glycosyltransferases : Cationic patches and anionic lipids regulate biomembrane binding of both GT-A and GT-B enzymes

This thesis concerns work on structure and membrane interactions of enzymes involved in lipid synthesis, biomembrane and cell wall regulation and cell defense processes. These proteins, known as glycosyltransferases (GTs), are involved in the transfer of sugar moieties from nucleotide sugars to lipids or chitin polymers. Glycosyltransferases from three types of organisms have been investigated; one is responsible for vital lipid synthesis in Arabidopsis thaliana (atDGD2) and adjusts the lipid content in biomembranes if the plant experiences stressful growth conditions. This enzyme shares many structural features with another GT found in gram-negative bacteria (WaaG). WaaG is however continuously active and involved in synthesis of the protective lipopolysaccharide layer in the cell walls of Escherichia coli. The third type of enzymes investigated here are chitin synthases (ChS) coupled to filamentous growth in the oomycete Saprolegnia monoica. I have investigated two ChS-derived MIT domains that may be involved in membrane interactions within the endosomal pathway. From analysis of the three-dimensional structure and the amino-acid sequence, some important regions of these very large proteins were selected for in vitro studies. By the use of an array of biophysical methods (e.g. Nuclear Magnetic Resonance, Fluorescence and Circular Dichroism spectroscopy) and directed sequence analyses it was possible to shed light on some important details regarding the structure and membrane-interacting properties of the GTs. The importance of basic amino-acid residues and hydrophobic anchoring segments, both generally and for the abovementioned proteins specifically, is discussed. Also, the topology and amino-acid sequence of GT-B enzymes of the GT4 family are analyzed with emphasis on their biomembrane association modes. The results presented herein regarding the structural and lipid-interacting properties of GTs aid in the general understanding of glycosyltransferase activity. Since GTs are involved in a high number of biochemical processes in vivo it is of outmost importance to understand the underlying processes responsible for their activity, structure and interaction events. The results are likely to be useful for many applications and future experimental design within life sciences and biomedicine.

Conservation genetics of North Atlantic loggerhead sea turtles: analysis of nuclear and mitochondrial DNA

[EN] Complex population structure has been described for the loggerhead sea turtle (Caretta caretta), revealing lower levels of population genetic structure in nuclear compared to mitochondrial DNA assays. This may result from mating during spatially overlapping breeding migrations, or male-biased dispersal as previously found for the green turtle (Chelonia mydas). To further investigate these multiple possibilities, we carried out a comparative analysis from twelve newly developed microsatellite loci and the mitochondrial DNA control region (~804 bp) in adult females of the Cape Verde Islands (n=158), and Georgia, USA (n=17).

Efectos de la microestructura sobre la transmisión de neutrones en materiales de interés nuclear.

Cuando un haz policromático de neutrones pasa a través de un material, los neutrones de distintas longitudes de onda son atenuados en formas muy diferentes. Como resultado, el espectro de energía del haz de neutrones cambia cuando una muestra es colocada frente el haz. Un análisis detallado del cociente de intensidad entre los haces de transmitido e incidente puede proporcionar una gran cantidad de información acerca de la estructura cristalina y microestructura de la muestra, definidas a través de la sección eficaz total del material. Para neutrones térmicos y sub-térmicos, el ordenamiento y movimiento de los átomos a escala microscópica define en forma precisa la dependencia de esta magnitud con la energía del neutrón incidente. Así, la variación con la energía de la sección eficaz total de los sólidos debido a la estructura de los átomos para distancias entre 0,1 y 100 Å se encuentra bien establecida, y es explotada en el estudio de estructuras cristalinas y de los movimientos vibracionales y rotacionales. Como contrapartida, el efecto de la estructura mesoscópica de los materiales, esto es para dimensiones entre 0,1 y 100 µm, sobre la sección eficaz total ha sido mucho menos estudiado, a pesar de provocar cambios profundos en esta magnitud. En esta Tesis estudiamos y formalizamos la dependencia de la sección eficaz total con características microestructurales tales como la porosidad, y la distribución de tamaños y orientaciones de los granos que componen los materiales, y desarrollamos modelos teóricos a partir de las características microestructurales de muestras de interés nuclear con diferente microestructura. Estos modelos permiten describir la contribuci ón de la componente elástica coherente de la seción eficaz total sobre los espectros de transmisión de neutrones e introducen parámetros como la cantidad de cristales que conforman el material, su estructura cristalina, parámetros de red, mosaicidad, estructura de poros u orientación preferencial de granos, para describir la sección total de materiales monocristalinos o policristalinos. En todos los casos, los modelos desarrollados fueron implementados en una biblioteca basada en el lenguaje computacional MATLAB y fueron comparados con secciones eficaces totales obtenidas en experimentos de transmisión de neutrones realizados en el Departamento de Física de Neutrones del Centro Atómico Bariloche y en ISIS Facility, Reino Unido. Los novedosos modelos microestructurales propuestos describen fielmente los experimentos desarrollados sobre muestras con distinta microestructura, lo que permite el empleo de los mismos en un código de refinamiento sobre los datos experimentales. Aquí, desarrollamos herramientas computacionales que ajustan por cuadrados mínimos no lineales los modelos paramétricos representativos de cada microestructura, sobre la sección eficaz total o la transmisión experimental, para determinar parámetros microestructurales de la muestra a partir de experimentos de transmisión de neutrones con resolución en longitud de onda. Los resultados son de particular relevancia para la interpretación y el análisis cuantitativo de las imágenes realizadas por la técnica de radiografía neutrónica con resolución en energía, que ha recibido un gran impulso en años recientes.

Air Pollution and High Density Lipoprotein Structure and Function

Thesis (Ph.D.)--University of Washington, 2016-06

Structure morphologique et populations stellaires d’un échantillon de galaxies spirales

Afin de caractériser la structure morphologique et les populations stellaires d’un échantillon de treize galaxies spirales, j’ai analysé des images WISE et GALEX, et j’ai construit des diagrammes magnitude-magnitude et couleur-magnitude pixel à pixel. Les diagrammes présentent des groupes de pixels qui correspondent spatialement aux composantes structurales des galaxies. Les diagrammes ainsi que les profils radiaux de brillance de surface indiquent que les variations de la densité surfacique de masse de la vieille population stellaire jouent un rôle important dans la différenciation des structures. On estime l’âge des jeunes complexes stellaires et l’extinction dans ces galaxies en les comparant à des modèles de populations stellaires simples nées de sursauts de formation stellaire instantanée. L’étude de ces propriétés est possible grâce à la combinaison des données ultraviolettes et infrarouge et à la grande sensibilité de la couleur ultraviolette à la variation de l’âge. On observe un gradient d’extinction dont la pente est liée à la présence d’une barre ou d’une activité nucléaire : en effet, l’extinction décroît avec la distance galactocentrique et la pente est plus petite pour les galaxies ayant une barre ou une activité nucléaire. On observe également un gradient d’âge où les régions externes sont moins évoluées que celles du centre sauf pour les galaxies de type tardif.

Efectos de la microestructura sobre la transmisión de neutrones en materiales de interés nuclear.

Cuando un haz policromático de neutrones pasa a través de un material, los neutrones de distintas longitudes de onda son atenuados en formas muy diferentes. Como resultado, el espectro de energía del haz de neutrones cambia cuando una muestra es colocada frente el haz. Un análisis detallado del cociente de intensidad entre los haces de transmitido e incidente puede proporcionar una gran cantidad de información acerca de la estructura cristalina y microestructura de la muestra, definidas a través de la sección eficaz total del material. Para neutrones térmicos y sub-térmicos, el ordenamiento y movimiento de los átomos a escala microscópica define en forma precisa la dependencia de esta magnitud con la energía del neutrón incidente. Así, la variación con la energía de la sección eficaz total de los sólidos debido a la estructura de los átomos para distancias entre 0,1 y 100 Å se encuentra bien establecida, y es explotada en el estudio de estructuras cristalinas y de los movimientos vibracionales y rotacionales. Como contrapartida, el efecto de la estructura mesoscópica de los materiales, esto es para dimensiones entre 0,1 y 100 µm, sobre la sección eficaz total ha sido mucho menos estudiado, a pesar de provocar cambios profundos en esta magnitud. En esta Tesis estudiamos y formalizamos la dependencia de la sección eficaz total con características microestructurales tales como la porosidad, y la distribución de tamaños y orientaciones de los granos que componen los materiales, y desarrollamos modelos teóricos a partir de las características microestructurales de muestras de interés nuclear con diferente microestructura. Estos modelos permiten describir la contribuci ón de la componente elástica coherente de la seción eficaz total sobre los espectros de transmisión de neutrones e introducen parámetros como la cantidad de cristales que conforman el material, su estructura cristalina, parámetros de red, mosaicidad, estructura de poros u orientación preferencial de granos, para describir la sección total de materiales monocristalinos o policristalinos. En todos los casos, los modelos desarrollados fueron implementados en una biblioteca basada en el lenguaje computacional MATLAB y fueron comparados con secciones eficaces totales obtenidas en experimentos de transmisión de neutrones realizados en el Departamento de Física de Neutrones del Centro Atómico Bariloche y en ISIS Facility, Reino Unido. Los novedosos modelos microestructurales propuestos describen fielmente los experimentos desarrollados sobre muestras con distinta microestructura, lo que permite el empleo de los mismos en un código de refinamiento sobre los datos experimentales. Aquí, desarrollamos herramientas computacionales que ajustan por cuadrados mínimos no lineales los modelos paramétricos representativos de cada microestructura, sobre la sección eficaz total o la transmisión experimental, para determinar parámetros microestructurales de la muestra a partir de experimentos de transmisión de neutrones con resolución en longitud de onda. Los resultados son de particular relevancia para la interpretación y el análisis cuantitativo de las imágenes realizadas por la técnica de radiografía neutrónica con resolución en energía, que ha recibido un gran impulso en años recientes.

Yang–Mills solutions and dyons on cylinders over coset spaces with Sasakian structure

We present solutions of the Yang–Mills equation on cylinders R×G/HR×G/H over coset spaces of odd dimension 2m+12m+1 with Sasakian structure. The gauge potential is assumed to be SU(m)SU(m)-equivariant, parameterized by two real, scalar-valued functions. Yang–Mills theory with torsion in this setup reduces to the Newtonian mechanics of a point particle moving in R2R2 under the influence of an inverted potential. We analyze the critical points of this potential and present an analytic as well as several numerical finite-action solutions. Apart from the Yang–Mills solutions that constitute SU(m)SU(m)-equivariant instanton configurations, we construct periodic sphaleron solutions on S1×G/HS1×G/H and dyon solutions on iR×G/HiR×G/H.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.

Connectivity patterns inferred from the genetic structure of white seabream (Diplodus sargus L.)

Themarine environment seems, at first sight, to be a homogeneousmediumlacking barriers to species dispersal. Nevertheless, populations of marine species show varying levels of gene flow and population differentiation, so barriers to gene flow can often be detected. Weaimto elucidate the role of oceanographical factors ingenerating connectivity among populations shaping the phylogeographical patterns in the marine realm, which is not only a topic of considerable interest for understanding the evolution ofmarine biodiversity but also formanagement and conservation of marine life. For this proposal,we investigate the genetic structure and connectivity between continental and insular populations ofwhite seabreamin North East Atlantic (NEA) and Mediterranean Sea (MS) aswell as the influence of historical and contemporary factors in this scenario using mitochondrial (cytochrome b) and nuclear (a set of 9 microsatellite) molecular markers. Azores population appeared genetically differentiated in a single cluster using Structure analysis. This result was corroborated by Principal Component Analysis (PCA) and Monmonier algorithm which suggested a boundary to gene flow, isolating this locality. Azorean population also shows the highest significant values of FST and genetic distances for both molecular markers (microsatellites and mtDNA). We suggest that the breakdown of effective genetic exchange between Azores and the others' samples could be explained simultaneously by hydrographic (deep water) and hydrodynamic (isolating current regimes) factors acting as barriers to the free dispersal of white seabream(adults and larvae) and by historical factors which could be favoured for the survival of Azorean white seabream population at the last glaciation. Mediterranean islands show similar genetic diversity to the neighbouring continental samples and nonsignificant genetic differences. Proximity to continental coasts and the current system could promote an optimal larval dispersion among Mediterranean islands (Mallorca and Castellamare) and coasts with high gene flow.

Nuclear Magnetic Resonance Spectroscopic and Computational Investigations of Chloroperoxidase Catalyzed Regio- and Enantio-Selective Transformations

Chloroperoxidase (CPO) is the most versatile heme-containing enzyme that catalyzes a broad spectrum of reactions. The remarkable feature of this enzyme is the high regio- and enantio-selectivity exhibited in CPO-catalyzed oxidation reactions. The aim of this dissertation is to elucidate the structural basis for regio- and enantio-selective transformations and investigate the application of CPO in biodegradation of synthetic dyes. To unravel the mechanism of CPO-catalyzed regioselective oxidation of indole, the dissertation explored the structure of CPO-indole complex using paramagnetic relaxation and molecular modeling. The distances between the protons of indole and the heme iron revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. This provides the first experimental and theoretical explanation for the "unexpected" regioselectivity of CPO-catalyzed indole oxidation. Furthermore, the residues including Leu 70, Phe 103, Ile 179, Val 182, Glu 183, and Phe 186 were found essential to the substrate binding to CPO. These results will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications. To understand the origin of the enantioselectivity of CPO-catalyzed oxidation reactions, the interactions of CPO with substrates such as 2-(methylthio)thiophene were investigated by nuclear magnetic resonance spectroscopy (NMR) and computational techniques. In particular, the enantioselectivity is partly explained by the binding orientation of substrates. In third facet of this dissertation, a green and efficient system for degradation of synthetic dyes was developed. Several commercial dyes such as orange G were tested in the CPO-H2O2-Cl- system, where degradation of these dyes was found very efficient. The presence of halide ions and acidic pH were found necessary to the decomposition of dyes. Significantly, the results revealed that this degradation of azo dyes involves a ferric hypochlorite intermediate of CPO (Fe-OCl), compound X.

“Acid-spike” effect in spurs/tracks of the low/high linear energy transfer radiolysis of water : potential implications for radiobiology and nuclear industry

Résumé : Les ions hydronium (H3O + ) sont formés, à temps courts, dans les grappes ou le long des trajectoires de la radiolyse de l'eau par des rayonnements ionisants à faible transfert d’énergie linéaire (TEL) ou à TEL élevé. Cette formation in situ de H3O + rend la région des grappes/trajectoires du rayonnement temporairement plus acide que le milieu environnant. Bien que des preuves expérimentales de l’acidité d’une grappe aient déjà été signalées, il n'y a que des informations fragmentaires quant à son ampleur et sa dépendance en temps. Dans ce travail, nous déterminons les concentrations en H3O + et les valeurs de pH correspondantes en fonction du temps à partir des rendements de H3O + calculés à l’aide de simulations Monte Carlo de la chimie intervenant dans les trajectoires. Quatre ions incidents de différents TEL ont été sélectionnés et deux modèles de grappe/trajectoire ont été utilisés : 1) un modèle de grappe isolée "sphérique" (faible TEL) et 2) un modèle de trajectoire "cylindrique" (TEL élevé). Dans tous les cas étudiés, un effet de pH acide brusque transitoire, que nous appelons un effet de "pic acide", est observé immédiatement après l’irradiation. Cet effet ne semble pas avoir été exploré dans l'eau ou un milieu cellulaire soumis à un rayonnement ionisant, en particulier à haut TEL. À cet égard, ce travail soulève des questions sur les implications possibles de cet effet en radiobiologie, dont certaines sont évoquées brièvement. Nos calculs ont ensuite été étendus à l’étude de l'influence de la température, de 25 à 350 °C, sur la formation in situ d’ions H3O + et l’effet de pic acide qui intervient à temps courts lors de la radiolyse de l’eau à faible TEL. Les résultats montrent une augmentation marquée de la réponse de pic acide à hautes températures. Comme de nombreux processus intervenant dans le cœur d’un réacteur nucléaire refroidi à l'eau dépendent de façon critique du pH, la question ici est de savoir si ces fortes variations d’acidité, même si elles sont hautement localisées et transitoires, contribuent à la corrosion et l’endommagement des matériaux.

The genetic diversity of the American oil palm, Elaeis oleifera (Kunth), Cortes revealed by nuclear RFLP markers.

The genetic diversity of E. oleifera is strongly structured by geographical origin, with four groups clearly distinguished: Brazil, Surinam/French Guyana, north of /Colombia/Central America and Peru. Within the Amazon basin, thereis a moderate structure that corresponds to the major tributaries of the Amazon river. From the 37 polymorphic RFLP probe/enzyme combinatios used, 19 probes (51%) presented simple restriction profiles, with one (1) or two bands/plant, suggesting a single locus with different alleles, allowing allelic co-dominant coding for them.

The foodomics approach to investigate the impact of the matrix structure on food quality: applications of magnetic resonance spectroscopy, relaxometry and imaging

The aim of this thesis is to explore the possible influence of the food matrix on food quality attributes. Using nuclear magnetic resonance techniques, the matrix-dependent properties of different foods were studied and some useful indices were defined to classify food products based on the matrix behaviour when responding to processing phenomena. Correlations were found between fish freshness indices, assessed by certain geometric parameters linked to the morphology of the animal, i.e. a macroscopic structure, and the degradation of the product structure. The same foodomics approach was also applied to explore the protective effect of modified atmospheres on the stability of fish fillets, which are typically susceptible to oxidation of the polyunsaturated fatty acids incorporated in the meat matrix. Here, freshness is assessed by evaluating the time-dependent change in the fish metabolome, providing an established freshness index, and its relationship to lipid oxidation. In vitro digestion studies, focusing on food products with different matrixes, alone and in combination with other meal components (e.g. seasoning), were conducted to investigate possible interactions between enzymes and food, modulated by matrix structure, which influence digestibility. The interaction between water and the gelatinous matrix of the food, consisting of a network of protein gels incorporating fat droplets, was also studied by means of nuclear magnetic relaxometry, in order to create a prediction tool for the correct classification of authentic and counterfeit food products protected by a quality label. This is one of the first applications of an NMR method focusing on the supramolecular structure of the matrix, rather than the chemical composition, to assess food authenticity. The effect of innovative processing technologies, such as PEF applied to fruit products, has been assessed by magnetic resonance imaging, exploiting information associated with the rehydration kinetics exerted by a modified food structure.

Mitochondrial Inheritance, Mito-nuclear Coevolution, and Sex-associated Genes in Bivalve Molluscs: Transcriptomics and Molecular Evolution

Bivalvia represents an ancient taxon including around 25,000 living species that have adapted to a wide range of environmental conditions, and show a great diversity in body size, shell shapes, and anatomic structure. Bivalves are characterized by highly variable genome sizes and extremely high levels of heterozygosity, which obstacle complete and accurate genome assemblies and hinder further genomic studies. Moreover, some bivalve species presented a stable evolutionary exception to the strictly maternal inheritance of mitochondria, namely doubly uniparental inheritance (DUI), making these species a precious model to study mitochondrial biology. During my PhD, I focused on a DUI species, the Manila clam Ruditapes philippinarum, and my work was two-folded. First, taking advantage of a newly assembled draft genome and a large RNA-seq dataset from different tissues of both sexes, I investigated 1) the role of gene expression and alternative splicing in tissue differentiation; 2) the relationship across tissue specificity, regulatory network connectivity, and sequence evolution; 3) sexual contrasting genetic markers potentially associated with sexual differentiation. The detailed information for this part is in Chapter 2. Second, using the same RNA-seq data, I investigated how nuclear oxidative phosphorylation (OXPHOS) genes coordinate with two divergent mitochondrial genomes in DUI species (mito-nuclear coordination and coevolution). To address this question, I compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of R. philippinarum in Chapter 3. To my knowledge, this thesis represents the first study exploring the role of alternative splicing in tissue differentiation, and the first study analyzing both transcriptional regulation and sequence evolution to investigate the coordination of OXPHOS genes in bivalves.