NCR-PCOPGene: An Exploratory Tool for Analysis of Sample-Classes Effect on Gene-Expression Relationships

Background. Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data. Our tools allow researchers to test and formulate from a hypothesis to entire models. Results. The objective of the NCRPCOPGene is to study the relationships among gene expressions under different conditions, to classify these conditions, and to study their effect on the different relationships. The web application makes it easier to define the sample classes, grouping the microarray experiments either by using (a) biological, statistical, or any other previous knowledge or (b) their effect on the expression relationship maintained among specific genes of interest. By means of the type (a) class definition, the researcher can add biological information to the gene-expression relationships. The type (b) class definition allows for linking genes correlated neither linearly nor nonlinearly. Conclusions. The PCOPGene tools are especially suitable for microarrays with large sample series. This application helps to identify cellular states and the genes involved in it in a flexible way. The application takes advantage of the ability of our system to relate gene expressions; even when these relationships are noncontinuous and cannot be found using linear or nonlinear analytical methods

How hydrophobicity shapes the architecture of protein assemblies

Altres ajuts: acords transformatius de la UABThe interactions that give rise to protein self-assembly are basically electrical and hydrophobic in origin. The electrical interactions are approached in this study as the interaction between electrostatic dipoles originated by the asymmetric distribution of their charged amino acids. However, hydrophobicity is not easily derivable from basic physicochemical principles. Its treatment is carried out here considering a hydrophobic force field originated by "hydrophobic charges". These charges are indices obtained experimentally from the free energies of transferring amino acids from polar to hydrophobic media. Hydrophobic dipole moments are used here in a manner analogous to electric dipole moments, and an empirical expression of interaction energy between hydrophobic dipoles is derived. This methodology is used with two examples of self-assembly systems of different complexity. It was found that the hydrophobic dipole moments of proteins tend to interact in such a way that they align parallel to each other in a completely analogous way to how phospholipids are oriented in biological membranes to form the well-known double layer. In this biological membrane model (BM model), proteins tend to interact in a similar way, although in this case this alignment is modulated by the tendency of the corresponding electrostatic dipoles to counter-align

PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships

<p>Abstract</p> <p>Background</p> <p>Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data, specially from large-sample-series microarrays. Our web tools attempt to respond to these researchers' needs by facilitating the possibility to test and formulate from a hypothesis to entire models under a holistic point of view.</p> <p>Results</p> <p>PCOPGene-Net is a web application for facilitating the study of the relationships among gene expressions under microarray conditions, to classify these conditions and to study their effect on expression relationships. Furthermore, the system guides the researcher in the navigation through the microarray data by providing the most suitable genes and information for the researcher's interests at each moment. We achieve all of these by means of the zoom-out operation, the zoom-in operation, the non-continuous analysis and crossing the PCOPGene results with external data-servers.</p> <p>Conclusion</p> <p>PCOPGene-Net helps to identify cellular states and the genes involved in these. All of that is accomplished in a flexible way, guided by the researcher's interests and taking advantage of the ability of our system to relate gene expressions, even when these relationships are non-continuous and cannot be found using linear or non-linear analytical methods. Currently, our tools are used for tumour-progression study from a holistic point of view.</p

Influential factors in determination of biomass termal susceptibility by termal analysis

Las biomasas almacenadas en silos son potencialmente capaces de absorber oxígeno produciendo reacciones exotérmicas de oxidación. Si el calor producido en estas reacciones no se dispersa adecuadamente, provoca un auto-calentamiento de la materia orgánica que puede ser causa de descomposición e inflamación. En el ámbito de la posible auto-combustión en el almacenamiento y manipulación de las biomasas existen diversos factores que influyen en la susceptibilidad térmica de las biomasas, es decir, en su tendencia a la oxidación y posterior inflamación de la materia. Con el fin de analizar este comportamiento se han estudiado diferentes tipos de biomasas. En este estudio se ha trabajado con biomasas de origen agrícola, forestal y residual con distinta composición química. Las muestras de estudio se han acondicionado mediante distintos tratamientos físicos para valorar la influencia de diferentes factores en su auto-combustión

Experimental developments for measuring the initiation of mine fires

A scale model of a dead end gallery has been developed. After heated air flow was introduced, the increase in temperature and gases evolution were monitored. The ventilation was increased and the temperature was elevated to produce an ignition process. Obtained data have shown significant measures of the self ignition mechanism, bringing a valuable tool to predict and early detect the process

Quantitative Assessment of Mycoplasma Hemadsorption Activity by Flow Cytometry

A number of adherent mycoplasmas have developed highly complex polar structures that are involved in diverse aspects of the biology of these microorganisms and play a key role as virulence factors by promoting adhesion to host cells in the first stages of infection. Attachment activity of mycoplasma cells has been traditionally investigated by determining their hemadsorption ability to red blood cells and it is a distinctive trait widely examined when characterizing the different mycoplasma species. Despite the fact that protocols to qualitatively determine the hemadsorption or hemagglutination of mycoplasmas are straightforward, current methods when investigating hemadsorption at the quantitative level are expensive and poorly reproducible. By using flow cytometry, we have developed a procedure to quantify rapidly and accurately the hemadsorption activity of mycoplasmas in the presence of SYBR Green I, a vital fluorochrome that stains nucleic acids, allowing to resolve erythrocyte and mycoplasma cells by their different size and fluorescence. This method is very reproducible and permits the kinetic analysis of the obtained data and a precise hemadsorption quantification based on standard binding parameters such as the dissociation constant Kd. The procedure we developed could be easily implemented in a standardized assay to test the hemadsorption activity of the growing number of clinical isolates and mutant strains of different mycoplasma species, providing valuable data about the virulence of these microorganisms

Application of protection means against explosions in underground mines

Underground coal mines explosions generally arise from the inflammation of a methane/air mixture. This explosion can also generate a subsequent coal dust explosion. Traditionally such explosions have being fought eliminating one or several of the factors needed by the explosion to take place. Although several preventive measures are taken to prevent explosions, other measures should be considered to reduce the effects or even to extinguish the flame front. Unlike other protection methods that remove one or two of the explosion triangle elements, namely; the ignition source, the oxidizing agent and the fuel, explosion barriers removes all of them: reduces the quantity of coal in suspension, cools the flame front and the steam generated by vaporization removes the oxygen present in the flame. The present paper is essentially based on the comprehensive state-of–the-art of Protective Systems in underground coal mines, and particularly on the application of Explosion Barriers to improve safety level in Spanish coal mining industry. After an exhaustive study of series EN 14591 standards covering explosion prevention and protection in underground mines, authors have proven explosion barriers effectiveness in underground galleries by Full Scale Tests performed in Polish Barbara experimental mine, showing that the barriers can reduce the effects of methane and/or flammable coal dust explosions to a satisfactory safety level

Una experiencia de aplicación de mapas conceptuales en la enseñanza de química física

En este trabajo se ha analizado de qué manera los alumnos de tercer curso de la ETSIM (UPM) elaboran mapas conceptuales en la enseñanza de la asignatura de Química Física. Antes de impartir el tema sobre corrosión los investigadores evaluaron los conocimientos previos de los estudiantes y los iniciaron en la construcción de los mapas conceptuales. Al final del curso los alumnos elaboraron un mapa conceptual. Los resultados obtenidos evidenciaron que la estrategia utilizada para iniciar a los alumnos en la construcción de mapas conceptuales fue eficiente, permitiéndoles aprender a trabajar con esta herramienta

Study of porosity and permeability of air filter material in respiratory proptection filters.

The objective is the study of filtering tissue permeability and the characterization by means of permeability tests, of the process of coal particles retention in breath protection filters.The permeability of nine probes have been measured against partic

Caracterización de un proteoma mínimo: Mycoplasma genitalium

Comunicaciones a congreso