Multiresponsive supramolecular systems for information processing at the molecular level

Dissertação para obtenção do Grau de Doutor em Química Sustentável

Studies of the assembly of the Streptococcus pneumoniae capsular polysaccharide

Dissertation presented to obtain the Ph.D degree in Biology.

Supercomplexes of Prokaryotic Aerobic Respiratory Chains-Escherichia coli and Bacillus subtilis supramolecular assemblies

Dissertation presented to obtain the Ph.D degree in Biochemistry.

Assembly and function of a protein cross-linking enzyme during bacterial spore morphogenesis

Sporulation in Bacillus subtilis culminates with the formation of a dormant endospore. The endospore (or spore) is one of the most resilient cell types known and can remain viable in the environment for extended periods of time. Contributing to the spore’s resistance and its ability to interact with and monitor its immediate environment is the coat, the outermost layer of B. subtilis spores. The coat is composed by over 70 different proteins, which are produced at different stages in sporulation and orderly assembled around the developing spore.(...)

Single line for assembly just-in-sequence multiple models

Programa Doutoral em Líderes para as Indústrias Tecnológicas

Regulación supramolecular de la dinámica de biomembranas por Esfingolípidos y Fosfolípidos

Los cambios que ocurren durante el funcionamiento (normal o patológico) de biomembranas resultan de alteraciones de interacciones moleculares dinámicas. Éstas involucran a fenómenos supramoleculares críticos (cambios de fase, electrostáticos y topológicos) que regulan la organización, estabilidad, expresión y metabolismo de lípidos y proteínas de membrana. Para conocer los factores físico-químicos que controlan el comportamiento de biomembranas se deben utilizar técnicas que permitan un control preciso de la organización molecular. (...) Objetivos generales y específicos: El propósito a largo plazo de las investigaciones es establecer las bases moleculares y supramoleculares por las cuales interacciones entre esfingolípidos, fosfolípidos y sus derivados regulan la organización, reconocimiento y reactividad de biomembranas. Al presente se estudia: I) Control supramolecular de la catálisis enzimática interfacial por enzimas fosfohidrolíticas que median la transducción de señales a nivel de membrana. II) Modulación de la estabilidad de biomembranas por cambios críticos de composición de la interfase, interacciones y transiciones topológicas. III) Caracterización y transferencia a soportes sólidos y líquidos de capas monomoleculares de organización intermolecular controlada, formadas con membranas neuronales y gliales.

Sensores basados en nanocavidades de sistemas supramoleculares. Sensors based on nanocavities of supramolecular systems.

Uno de los grandes desafíos analíticos es resolver la complejidad del análisis de cantidades trazas de compuestos orgánicos debido a la baja sensibilidad analítica de las técnicas usuales que permiten una determinación específica como IR o RMN. El uso de espectrofotometría UV-Visible y espectroluminiscencia, técnicas que presentan mayor sensibilidad, se ve dificultada en muchos casos por el efecto matriz producido en el tratamiento de muestras reales y complejas o pérdida de la selectividad debido a la superposición de bandas.La interacción por formación de complejos entre determinados sustratos y receptores macrocíclicos que presentan poros o cavidades nanométricas, puede afectar las propiedades espectroscópicas de los sustratos. La respuesta de técnicas sensibles puede traducirse así en un análisis selectivo debido al reconocimiento molecular que se establece entre un dado receptor y el sustrato de interés. Por otra parte puede mejorar la sensibilidad debido a efectos de micropolaridad del medio, a efectos de restricciones de grados de libertad, por compartamentalización o protección de los estados excitados de los sustratos incluidos. El uso analítico de receptores selectivos es un área actualmente en desarrollo, que permite una rápida determinación de especies químicas, disminuyendo el efecto de interferentes, mejorando la sensibilidad y disminuyendo el tratamiento de la muestra.Se estudiarán los mecanismos involucrados en las interacciones y los factores que los modifican por técnicas espectroscópicas como UV-visible, RMN y luminiscencia. Se determinarán los parámetros analíticos por luminiscencia en los medios y condiciones en que la sensibilidad analítica muestre el mayor incremento. Se realizarán las pruebas de validación en las mejores condiciones para cada uno y mezclas de analitos relacionados en muestras reales.

Kinetics of methanol electrooxidation on PtRu catalysts in a membrane electrode assembly

Methanol oxidation, Kinetics, Mechanism, Rate expression, MEA, PtRu catalysts, Cyclone Flow Cell

Mechanisms of assembly and activity dependent remodelling of the presynaptic cytomatrix at the active zone

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2010

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Profiling of T-cell receptor signaling complex assembly in human CD4 T-lymphocytes using RP protein arrays.

The RP protein (RPP) array approach immobilizes minute amounts of cell lysates or tissue protein extracts as distinct microspots on NC-coated slide. Subsequent detection with specific antibodies allows multiplexed quantification of proteins and their modifications at a scale that is beyond what traditional techniques can achieve. Cellular functions are the result of the coordinated action of signaling proteins assembled in macromolecular complexes. These signaling complexes are highly dynamic structures that change their composition with time and space to adapt to cell environment. Their comprehensive analysis requires until now relatively large amounts of cells (>5 x 10(7)) due to their low abundance and breakdown during isolation procedure. In this study, we combined small scale affinity capture of the T-cell receptor (TCR) and RPP arrays to follow TCR signaling complex assembly in human ex vivo isolated CD4 T-cells. Using this strategy, we report specific recruitment of signaling components to the TCR complex upon T-cell activation in as few as 0.5 million of cells. Second- to fourth-order TCR interacting proteins were accurately quantified, making this strategy specially well-suited to the analysis of membrane-associated signaling complexes in limited amounts of cells or tissues, e.g., ex vivo isolated cells or clinical specimens.

Preferential assembly of epithelial sodium channel (ENaC) subunits in Xenopus oocytes: role of furin-mediated endogenous proteolysis.

The epithelial sodium channel (ENaC) is preferentially assembled into heteromeric alphabetagamma complexes. The alpha and gamma (not beta) subunits undergo proteolytic cleavage by endogenous furin-like activity correlating with increased ENaC function. We identified full-length subunits and their fragments at the cell surface, as well as in the intracellular pool, for all homo- and heteromeric combinations (alpha, beta, gamma, alphabeta, alphagamma, betagamma, and alphabetagamma). We assayed corresponding channel function as amiloride-sensitive sodium transport (I(Na)). We varied furin-mediated proteolysis by mutating the P1 site in alpha and/or gamma subunit furin consensus cleavage sites (alpha(mut) and gamma(mut)). Our findings were as follows. (i) The beta subunit alone is not transported to the cell surface nor cleaved upon assembly with the alpha and/or gamma subunits. (ii) The alpha subunit alone (or in combination with beta and/or gamma) is efficiently transported to the cell surface; a surface-expressed 65-kDa alpha ENaC fragment is undetected in alpha(mut)betagamma, and I(Na) is decreased by 60%. (iii) The gamma subunit alone does not appear at the cell surface; gamma co-expressed with alpha reaches the surface but is not detectably cleaved; and gamma in alphabetagamma complexes appears mainly as a 76-kDa species in the surface pool. Although basal I(Na) of alphabetagamma(mut) was similar to alphabetagamma, gamma(mut) was not detectably cleaved at the cell surface. Thus, furin-mediated cleavage is not essential for participation of alpha and gamma in alphabetagamma heteromers. Basal I(Na) is reduced by preventing furin-mediated cleavage of the alpha, but not gamma, subunits. Residual current in the absence of furin-mediated proteolysis may be due to non-furin endogenous proteases.

TRAIP is a regulator of the spindle assembly checkpoint.

Accurate chromosome segregation during mitosis is temporally and spatially coordinated by fidelity-monitoring checkpoint systems. Deficiencies in these checkpoint systems can lead to chromosome segregation errors and aneuploidy, and promote tumorigenesis. Here, we report that the TRAF-interacting protein (TRAIP), a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation, is localized close to mitotic chromosomes. Its knockdown in HeLa cells by RNA interference (RNAi) decreased the time of early mitosis progression from nuclear envelope breakdown (NEB) to anaphase onset and increased the percentages of chromosome alignment defects in metaphase and lagging chromosomes in anaphase compared with those of control cells. The decrease in progression time was corrected by the expression of wild-type but not a ubiquitin-ligase-deficient form of TRAIP. TRAIP-depleted cells bypassed taxol-induced mitotic arrest and displayed significantly reduced kinetochore levels of MAD2 (also known as MAD2L1) but not of other spindle checkpoint proteins in the presence of nocodazole. These results imply that TRAIP regulates the spindle assembly checkpoint, MAD2 abundance at kinetochores and the accurate cellular distribution of chromosomes. The TRAIP ubiquitin ligase activity is functionally required for the spindle assembly checkpoint control.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.