Entropy involved in fidelity of DNA replication

Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication.Comment: 25 pages, 5 figure

Rotor detection in atrial fibrillation

Atrial fibrillation (AF) is one of the most common arrhythmias in the clinical practice. Catheter ablation method was developed more than 20 years ago as an approach to terminate this rhythm disorder. Since its outbreak, this technique obtained international acceptance among the clinicians, and technological advances in this field increased its safety while reducing the procedure duration. However, there is no perfect AF treatment procedure described yet, since the understanding of the driving and sustaining AF mechanisms remains poor, with pulmonary vein isolation being the most common ablation strategy. Several theories try to explain the initiating and maintenance mechanisms of the AF, ranging from multiple wavelets propagating at random in the atria to ectopic focus fired from the pulmonary veins. Alternatively, spatiotemporal stable sources (rotors) have been proposed as the maintenance mechanism of AF. The most representative characteristic of a rotor is the re-entry spiral-like propagation pattern that the electrical wavefront exhibits as it propagates. The assessment of its presence and posterior ablation of the sites where rotors anchor might improve the success of AF ablation. Technical solutions emerged focusing on the rotor assessment problem. They base their methods on the reconstruction of the atrial activity using multi-electrode catheters and phase maps, in which they detect singularity points, the sites where rotors spin. The ablation of these sites showed promising results, but the difficulty to reproduce the results by other authors increased the controversy on this technique. In this Thesis we address the rotor detection problem in the time domain as opposed to current methods based on the phase domain of the signals. We develop a new method to identify local activation times (LATs) in unipolar electrograms (EGMs) recorded with multi-electrode catheters. We propose a new filtering scheme to enhance the activation component of the EGM while considerably reducing the presence of noise in the signal. This signal processing method reects the real activity of the tissue in contact with the electrode. It opposes the Hilbert transform (HT) used to extract the phase component of the signal, that do not correlate well with the temporal activations. With the EGM LATs we perform a spatial interpolation translating the electrode positions of the catheter into a regular 2D grid. This way we generate isochronal maps revealing the electrical wavefronts in the atrium. What is more, this step guarantees compatibility with multi-electrode catheters, not restricting the method to specific models. With the isochronal maps, we develop a new rotor detection algorithm based on the optical flow of the wavefront dynamics, and a rotation pattern match. Additionally, we develop a new method based on Granger's causality to estimate the directionality of the wavefronts, that provides an additional indicator for rotational patterns. We validate the methods using in silico and real AF signals. We implement these methods into a system that can assess the presence of rotational activation sites in the atrium. Our system is able to operate in realtime with multi-electrode catheters of different topologies in contact with the atrial wall. We integrate signal acquisition and processing in our system, allowing direct acquisition of the signals without requiring signal exportation from a recording device, which delays the clinical procedure. We address the computational time handicap by designing parallelizable signal processing steps. We employ multi-core processors and GPU based code to distribute the computations and minimize the processing times, achieving near real-time results. The results presented in this Thesis provide a new technical solution to detect the presence of rotational activity (rotors) in AF patients in real-time. Although the presence of rotational activity is itself controversial, we individually validate each of the steps of the procedure and obtain evidence of the presence of rotational activity in AF patients. The system has been also found useful to characterize the atrial sites where rotational activity was found in terms of spatial and voltage distribution. The results of this Thesis provide a new alternative to existing methods based on phase analysis and open a new research line in the detection of the mechanisms sustaining AF.La fibrilación auricular (FA) es una de las arritmias más comunes en la práctica clínica. Para tratar de terminar esta fibrilación en pacientes se desarrollo el método de ablación con catéter hace ya más de 20 años. Desde su puesta en marchar esta técnica ha ido ganando aceptación internacional por parte de la comunidad médica, y los avances tecnológicos desarrollados en esta línea han aumentado la seguridad y disminuido la duración del procedimiento. Sin embargo todavía no existe un tratamiento perfecto para tratar la FA, debido en parte a que el conocimiento de los mecanismos que inician y sostienen la fibrilación son limitados. Como método de ablación el aislamiento de las venas pulmonares prevalece como el más empleado en la práctica, pero se hace necesario el desarrollo de nuevos métodos para hacer frente al problema de la FA. Distintas teorías tratan de explicar los mecanismos de inicio y mantenimiento de la FA, desde unas basadas en la propagación de múltiples frentes de onda aleatorios en las aurículas, hasta las que basan su hipótesis en focos ectópicos disparados principalmente desde las venas pulmonares, entre otras teorías. Recientemente, una de estas teorías basada en fuentes espacio-temporalmente estables (rotores) se propuso como mecanismo de mantenimiento de la FA. La característica más representativa de un rotor es su patrón de reentrada en forma de espiral que realiza el frente de onda eléctrico en el tejido auricular. La evaluación de la presencia de rotores y la posterior de los sitios en los que se encuentren puede mejorar el éxito de la ablación en pacientes con FA. En vista de esta tendencia por la búsqueda de rotores se desarrollaron soluciones técnicas para la evaluación de zonas que alberguen actividad rotacional. Sus técnicas se basan en la reconstrucción de la actividad auricular empleando catéteres multi-electrodo y detectando puntos de singularidad en mapas de phase, esto es la posición en la aurícula en la que el rotor gira. La ablación de estos puntos mostró resultados prometedores, pero la dificultad por replicar los resultados por parte de otros autores incremento la controversia con respecto a esta técnica. En esta Tesis abordamos el problema de la detección de rotores en el dominio del tiempo, oponiéndonos a las técnicas actuales basadas en el dominio de la fase de las señales. Para ello hemos desarrollado un nuevo para identificar tiempos de activación local en electrogramas unipolares registrados con catéteres multi-electrodo. Para ello proponemos un nuevo método de filtrado para realzar la activación del electrograma reduciendo considerablemente la presencia de ruido en la señal. Con este procesado de la señal extraemos y reflejamos la actividad real del tejido en contacto con el electrodo. Al mismo tiempo nos oponemos a la transformada de Hilbert empleada para calcular la componente de fase de la señal, que es sabido no tiene una buena correlación con las activaciones temporales. Con los electrogramas y los tiempos de activación locales aplicamos una interpolación espacial logrando trasladar la posición de los electrodos en el catéter a una rejilla regular en 2D. Mediante este paso generamos mapas isócronos que reconstruyen los frentes de onda eléctricos que se propagan en la aurícula. Además, la interpolación nos permite garantizar una compatibilidad con otros catéteres multi-electrodos, no restringiendo el uso de nuestro método a modelos específicos. Con los mapas isócronos hemos desarrollado un nuevo algoritmo de detección de rotores basado en el flujo óptico de la dinámica del frente de onda que hacemos coincidir con un patrón de rotación. Adicionalmente hemos desarrollado un nuevo método basad en la causalidad propuesta por Granger para estimar la dirección de los frentes de propagación, que sirve como indicador adicional para encontrar patrones de activación rotacional. Hemos validado todos y cada uno de los métodos empleando señales in silico así como señales reales de pacientes con FA. En la parte de aplicación, hemos implementado los métodos en un sistema que evalúa la presencia de actividad rotacional en la aurícula. Nuestro sistema opera en tiempo real siendo compatible con catéteres multi-electrodo de diferentes topologías asegurando contacto con la pared auricular. Para evitar sobreextender el procedimiento clínico, hemos integrado las partes de adquisición y procesado de señal conjuntamente, lo que nos permite un registro de las señales directo sin viii necesidad de requerir un exportado adicional desde un sistema de registro. Para hacer frente al objetivo de presentar los resultados en tiempo real hemos diseñado todos los pasos de procesado de señal para que sean paralelizables. Para ello empleamos procesadores multinúcleo y código para ejecutar en tarjetas gráficas (GPUs) para distribuir las computaciones y minimizar el tiempo de procesado, logrando resultados en quasi tiempo real. Hemos empleado el sistema de detección de rotores para estudiar la distribución espacial y de voltaje de los sitios que muestran actividad rotacional en la aurícula. Aunque la presencia de actividad rotacional es en sí misma controvertida, hemos validad individualmente todos y cada uno de los pasos descritos obteniendo evidencia de la presencia de actividad rotacional en pacientes con FA.Programa Oficial de Doctorado en Multimedia y ComunicacionesPresidente: Pablo Laguna Lasaosa.- Secretario: Pablo Martínez Olmos.- Vocal: Batiste Andreu Martínez Climen

Techno-Economic Analysis of Rural 4th Generation Biomass District Heating

Biomass heating networks provide renewable heat using low carbon energy sources. They can be powerful tools for economy decarbonization. Heating networks can increase heating efficiency in districts and small size municipalities, using more efficient thermal generation technologies, with higher efficiencies and with more efficient emissions abatement technologies. This paper analyzes the application of a biomass fourth generation district heating, 4GDH (4th Generation Biomass District Heating), in a rural municipality. The heating network is designed to supply 77 residential buildings and eight public buildings, to replace the current individual diesel boilers and electrical heating systems. The development of the new fourth district heating generation implies the challenge of combining using low or very low temperatures in the distribution network pipes and delivery temperatures in existing facilities buildings. In this work biomass district heating designs based on third and fourth generation district heating network criteria are evaluated in terms of design conditions, operating ranges, effect of variable temperature operation, energy efficiency and investment and operating costs. The Internal Rate of Return of the different options ranges from 6.55% for a design based on the third generation network to 7.46% for a design based on the fourth generation network, with a 25 years investment horizon. The results and analyses of this work show the interest and challenges for the next low temperature DH generation for the rural area under analysis

Field trials of an improved cost-effective device for detecting peridomestic populations of Triatoma infestans (Hemiptera: Reduviidae) in rural Argentina

An improved device for detecting peridomestic Triatoma infestans consisting of one-liter recycled Tetra Brik milk boxes with a central structure was tested using a matched-pair study design in two rural areas in Argentina. In Olta (La Rioja), the boxes were installed beneath the thatched roofs and on the vertical wooden posts of each peridomestic structure. After a 5-month exposure, at least one of the recovered boxes detected 88% of the 24 T. infestans-positive sites, and 86% of the 7 negative sites by timed manual collections at baseline. In Amamá (Santiago del Estero), the boxes were paired with the best performing prototype tested before (shelter unit). After 3 months, some evidence of infestation was detected in 89% (boxes) and 79% (shelters) of 18-19 sites positive by timed collections, whereas 19% and 16% of 32 negative sites were positive, respectively. Neither device differed significantly in the qualitative or quantitative collection of every sign of infestation. The installation site did not modify significantly the boxes' sampling efficiency in both study areas. As the total cost of each box was half as expensive as each shelter unit, the boxes are thus the most cost-effective and easy-to-use tool for detecting peridomestic T. infestans currently available.Fil: Vazquez Prokopec, Gonzalo Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; ArgentinaFil: Ceballos, Leonardo A.. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; ArgentinaFil: Salomón, Oscar Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Centro Nacional de Diagnóstico e Investigaciones Endemo-epidémicas; ArgentinaFil: Gurtler, Ricardo Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentin

The role of sodium phosphate cotransporters in ectopic calcification

Phosphate plays a critical role in many vital cellular processes. Deviations from normal serum phosphate levels, including alterations in the extracellular phosphate/pyrophosphate ratio, can cause severe consequences, such as ectopic calcification. Cellular phosphate levels are tightly controlled by sodium phosphate cotransporters, underscoring their importance in cellular physiology. The role of sodium phosphate cotransporters in ectopic calcification requires further elucidation, taking into account their important role in the control of intracellular phosphate levels and the synthesis of ATP, the main source of extracellular pyrophosphate (a potent endogenous inhibitor of calcification). In this review, we discuss the roles of phosphate and pyrophosphate homeostasis in ectopic calcification, with a specific focus on phosphate transporters. We concentrate on the five known sodium-dependent phosphate transporters and review their localisation and regulation by external factors, and the effects observed in knockout studies and in naturally occurring mutations

Effect of isolation conditions on structural properties and surface behavior of soy-whey proteins

In this study, the impact of isolation conditions on structural and surface properties at the air/water interface of soy-whey proteins (SWP) was assessed. SWP were obtained by precipitation of soy-whey (at pH 4.5 or 8.0) with acetone or ammonium sulfate. Despite the fact that all SWP samples exhibited similar electrophoretic patterns, they showed different protein content (from 54.2 to 98.2% w/w). When precipitation was performed at pH 4.5, SWP samples evidenced a decrease of protein solubility (SP) and thermal stability, while the precipitation with acetone promoted the enrichment in polysaccharides and minerals. For all samples, intrinsic fluorescence, surface hydrophobicity and Fourier transform infrared (FTIR) studies revealed structural changes correlated to protein unfolding and aggregation processes. However, the surface behavior can be predicted from these studies mainly due to differences in surface hydrophobicity and the differential contribution of insoluble aggregates. The heating of SWP samples enhanced the surface activity, regardless of the pH of the raw material and the isolation method. These results can be useful as a reference research and as a starting point for industrial exploitation of proteins from soy wastewater.Fil: Ingrassia, Romina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Física de Rosario. Universidad Nacional de Rosario. Instituto de Física de Rosario; ArgentinaFil: Sobral, Pablo Antonio. Universidad Nacional de La Plata. Facultad de Ciencias Exactas; ArgentinaFil: Risso, Patricia Hilda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Física de Rosario. Universidad Nacional de Rosario. Instituto de Física de Rosario; ArgentinaFil: Palazolo, Gonzalo Gastón. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Investigación en Funcionalidad y Tecnología de Alimentos; ArgentinaFil: Wagner, Jorge Ricardo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Investigación en Funcionalidad y Tecnología de Alimentos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Purification and biological characterization of halocin H1 from Haloferax mediterranei M2a

The production of halocins, bacteriocin-like proteins of ecological significance, is a frequent characteristic of species from the family Halobacteriaceae. Halocin H1, produced by Haloferax mediterranei strain M2a, is a single 31-kDa polypeptide. Its purification was achieved by combining two chromatographic systems: Sepharose 4B linked to bacitracin followed by hydroxylapatite Bio-gel HTP. Halocin H1 required concentrations of NaCl higher than 1.5 M to maintain its activity. Haoarchaeal strains showed a differential degree of sensitivity to the action of this halocin