Structural and functional properties of genes involved in human cancer

Background: One of the main goals of cancer genetics is to identify the causative elements at the molecular level leading to cancer.Results: We have conducted an analysis of a set of genes known to be involved in cancer in order to unveil their unique features that can assist towards the identification of new candidate cancer genes. Conclusion: We have detected key patterns in this group of genes in terms of the molecular function or the biological process in which they are involved as well as sequence properties. Based on these features we have developed an accurate Bayesian classification model with which human genes have been scored for their likelihood of involvement in cancer.

Pathology and immune response of the blue mussel (Mytilus edulis L.) after an exposure to the harmful dinoflagellate Prorocentrum minimum

The harmful dinoflagellate Prorocentrum minimum has different effects upon various species of grazing bivalves, and these effects also vary with life-history stage. Possible effects of this dinoflagellate upon mussels have not been reported; therefore, experiments exposing adult blue mussels, Mytilus edulis, to P. minimum were conducted. Mussels were exposed to cultures of toxic P. minimum or benign Rhodomonas sp. in glass aquaria. After a short period of acclimation, samples were collected on day 0 (before the exposure) and after 3, 6, and 9 days of continuous-exposure experiment. Hemolymph was extracted for flow-cytometric analyses of hemocyte, immune-response functions, and soft tissues were excised for histopathology. Mussels responded to P. minimum exposure with diapedesis of hemocytes into the intestine, presumably to isolate P. minimum cells within the gut, thereby minimizing damage to other tissues. This immune response appeared to have been sustained throughout the 9-day exposure period, as circulating hemocytes retained hematological and functional properties. Bacteria proliferated in the intestines of the P. minimum-exposed mussels. Hemocytes within the intestine appeared to be either overwhelmed by the large number of bacteria or fully occupied in the encapsulating response to P. minimum cells; when hemocytes reached the intestine lumina, they underwent apoptosis and bacterial degradation. This experiment demonstrated that M. edulis is affected by ingestion of toxic P. minimum; however, the specific responses observed in the blue mussel differed from those reported for other bivalve species. This finding highlights the need to study effects of HABs on different bivalve species, rather than inferring that results from one species reflect the exposure responses of all bivalves.

Predicting cancer involvement of genes from heterogeneous data

Background: Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data. Results: We implemented a systematic method using the PIANA software that predicts cancer involvement of genes by integrating heterogeneous datasets. Specifically, we produced lists of genes likely to be involved in cancer by relying on: (i) protein-protein interactions; (ii) differential expression data; and (iii) structural and functional properties of cancer genes. The integrative approach that combines multiple sources of data obtained positive predictive values ranging from 23% (on a list of 811 genes) to 73% (on a list of 22 genes), outperforming the use of any of the data sources alone. We analyze a list of 20 cancer gene predictions, finding that most of them have been recently linked to cancer in literature. Conclusion: Our approach to identifying and prioritizing candidate cancer genes can be used to produce lists of genes likely to be involved in cancer. Our results suggest that differential expression studies yielding high numbers of candidate cancer genes can be filtered using protein interaction networks.

Assessing the impact of high-pressure processing on selected physical and biochemical attributes of white cabbage (Brassica oleracea L. var. capitata alba)

The aim of this study was to investigate the effect of combined pressure/temperature treatments (200, 400 and 600 MPa, at 20 and 40 °C) on key physical and chemical characteristics of white cabbage (Brassica oleracea L. var. capitata alba). Thermal treatment (blanching) was also investigated and compared with high-pressure processing (HPP). HPP at 400 MPa and 20–40 °C caused significantly larger colour changes compared to any other pressure or thermal treatment. All pressure treatments induced a softening effect, whereas blanching did not significantly alter texture. Both blanching and pressure treatments resulted in a reduction in the levels of ascorbic acid, effect that was less pronounced for blanching and HPP at 600 MPa and 20–40 °C. HPP at 600 MPa resulted in significantly higher total phenol content, total antioxidant capacity and total isothiocyanate content compared to blanching. In summary, the colour and texture of white cabbage were better preserved by blanching. However, HPP at 600 MPa resulted in significantly higher levels of phytochemical compounds. The results of this study suggest that HPP may represent an attractive technology to process vegetable-based food products that better maintains important aspects related to the content of health-promoting compounds. This may be of particular relevance to the food industry sector involved in the development of convenient novel food products with excellent functional properties

Transport i emmagatzematge de les àmfores en l'antiguitat:l'aportació de les ciències dels materials

[spa]Las ánforas son ejemplos claros de cerámicas utilitarias que requieren de unas características técnicas necesarias para cumplir su funcionalidad: servir de envase de almacenamiento y transporte. En este trabajo se propone el estudio del comportamiento funcional de estos envases a través de la evaluación de las propiedades mecánicas de resistencia y tenacidad a la fractura. Propiedades mecánicas, ámforas ibéricas, ámforas romanas, tecnología, funcionalidad.

Two component systems: physiological effect of a third component

Signal transduction systems mediate the response and adaptation of organisms to environmental changes. In prokaryotes, this signal transduction is often done through Two Component Systems (TCS). These TCS are phosphotransfer protein cascades, and in their prototypical form they are composed by a kinase that senses the environmental signals (SK) and by a response regulator (RR) that regulates the cellular response. This basic motif can be modified by the addition of a third protein that interacts either with the SK or the RR in a way that could change the dynamic response of the TCS module. In this work we aim at understanding the effect of such an additional protein (which we call ‘‘third component’’) on the functional properties of a prototypical TCS. To do so we build mathematical models of TCS with alternative designs for their interaction with that third component. These mathematical models are analyzed in order to identify the differences in dynamic behavior inherent to each design, with respect to functionally relevant properties such as sensitivity to changes in either the parameter values or the molecular concentrations, temporal responsiveness, possibility of multiple steady states, or stochastic fluctuations in the system. The differences are then correlated to the physiological requirements that impinge on the functioning of the TCS. This analysis sheds light on both, the dynamic behavior of synthetically designed TCS, and the conditions under which natural selection might favor each of the designs. We find that a third component that modulates SK activity increases the parameter space where a bistable response of the TCS module to signals is possible, if SK is monofunctional, but decreases it when the SK is bifunctional. The presence of a third component that modulates RR activity decreases the parameter space where a bistable response of the TCS module to signals is possible.

Effects of neurotrophins on synaptic protein expression in the visual cortex of dark reared rats.

Total lack of visual experience [dark rearing (DR)] is known to prolong the critical period and delay development of sensory functions in mammalian visual cortex. Recent results show that neurotrophins (NTs) counteract the effects of DR on functional properties of visual cortical cells and exert a strong control on critical period duration. NTs are known to modulate the development and synaptic efficacy of neurotransmitter systems that are affected by DR. However, it is still unknown whether the actions of NTs in dark-reared animals involve interaction with neurotransmitter systems. We have studied the effects of DR on the expression of key molecules in the glutamatergic and GABAergic systems in control and NT-treated animals. We have found that DR reduced the expression of the NMDA receptor 2A subunit and its associated protein PSD-95 (postsynaptic density-95), of GRIP (AMPA glutamate receptor interacting protein), and of the biosynthetic enzyme GAD (glutamic acid decarboxylase). Returning dark-reared animals to light for 2 hr restored normal expression of the above-mentioned proteins almost completely. NT treatment specifically counteracts DR effects; NGF acts primarily on the NMDA system, whereas BDNF acts primarily on the GABAergic system. Finally, the action of NT4 seems to involve both excitatory and inhibitory systems. These data demonstrate that different NTs counteract DR effects by modulating the expression of key molecules of the excitatory and inhibitory neurotransmitter systems

Pancreatic Cancer Cell Glycosylation Regulates Cell Adhesion and Invasion through the Modulation of a2b1 Integrin and E-Cadherin Function

In our previous studies we have described that ST3Gal III transfected pancreatic adenocarcinoma Capan-1 and MDAPanc-28 cells show increased membrane expression levels of sialyl-Lewis x (SLex) along with a concomitant decrease in α2,6-sialic acid compared to control cells. Here we have addressed the role of this glycosylation pattern in the functional properties of two glycoproteins involved in the processes of cancer cell invasion and migration, α2β1 integrin, the main receptor for type 1 collagen, and E-cadherin, responsible for cell-cell contacts and whose deregulation determines cell invasive capabilities. Our results demonstrate that ST3Gal III transfectants showed reduced cell-cell aggregation and increased invasive capacities. ST3Gal III transfected Capan-1 cells exhibited higher SLex and lower α2,6-sialic acid content on the glycans of their α2β1 integrin molecules. As a consequence, higher phosphorylation of focal adhesion kinase tyrosine 397, which is recognized as one of the first steps of integrin-derived signaling pathways, was observed in these cells upon adhesion to type 1 collagen. This molecular mechanism underlies the increased migration through collagen of these cells. In addition, the pancreatic adenocarcinoma cell lines as well as human pancreatic tumor tissues showed colocalization of SLex and E-cadherin, which was higher in the ST3Gal III transfectants. In conclusion, changes in the sialylation pattern of α2β1 integrin and E-cadherin appear to influence the functional role of these two glycoproteins supporting the role of these glycans as an underlying mechanism regulating pancreatic cancer cell adhesion and invasion

Deformation properties of the Barcelona-Catania-Paris (BCP) energy density functional

We explore the deformation properties of the newly postulated Barcelona-Catania-Paris (BCP) energy density functional (EDF). The results obtained for three isotope chains of Mg, Dy, and Ra are compared to the available experimental data as well as to the results of the Gogny-D1S force. Results for the fission barrier of 240Pu are also discussed.

Elaboració de membranes de fibra buida modificades amb nanopartícules metàl·liques per aplicacions catalítiques

Investigación producida a partir de una estancia en la Université Paul Sabatier, Toulouse III - CNRS, entre 2007 y 2009. Durante los últimos años la investigación centrada en nuevos materiales de tamaño nanoscòpico (nanopartículas, quantum dots, nanotubos de carbono,...) ha experimentado un crecimiento considerable debido a las especiales propiedades de los "nanoobjetos" con respecto a magnetismo, catálisis, conductividad eléctrica, etc ... Sin embargo, hoy en día todavía existen pocas aplicaciones de las nanopartículas en temas medioambientales. Uno de los motivos de esta situación es la posible toxicidad de los nanoobjetos, pero existe también una dificultad tecnológica dado que las nanopartículas tienden a agregarse y es muy difícil manipularlas sin que pierdan sus propiedades especiales. Así, aunque la preparación de materiales catalíticos nanoestructurados es muy interesante, es necesario definir nuevas estrategias para prepararlos. Este proyecto de investigación tiene como objetivo principal la preparación de nuevas membranas catalíticas con nanopartículas metálicas en el interior para aplicaciones de tratamiento de agua. La innovación principal de este proyecto consiste en que las nanopartículas no son introducidas en la matriz polimérica una vez preformadas sino que se hacen crecer en el interior de la matriz polimérica mediante una síntesis intermatricial. El único requisito es que la matriz polimérica contenga grupos funcionales capaces de interaccionar con los precursores de las nanopartículas. Una vez finalizado el proyecto se puede afirmar que se han logrado parte de los objetivos planteados inicialmente. Concreamente ha quedado demostrado que se pueden sintetizar nanopartículas metálicas de metales nobles (platino y paladio) en membranas de fibra hueca de micro- y ultrafiltración siguiendo dos metodologías diferentes: modificación fotoquímica de polímeros y deposición de multicapas de polielectrolitos. Los nuevos materiales son efectivos en la catálisis de reducción de un compuesto modelo (4-nitrofenol con borohidruro de sodio) y, en general, los resultados han sido satisfactorios. Sin embargo, se ha puesto de manifiesto que el uso de un reactivo que genera hidrógeno gas en contacto con la solución acuosa dificulta enormemente la implementación de la reacción catalítica al ser el medio de la membrana una matriz porosa. Así, como conclusión principal se puede decir que se han encontrado las limitaciones de esta aproximación y se sugieren dos posibilidades de continuidad: la utilización de las membranas sintetizadas en contactores gas-líquido o bien el estudio y optimización del sistema de membrana en configuración de membranas planas, un objetivo más asequible dada su menor complejidad. Esta investigación se ha realizado en el seno del “Laboratoire de Génie Chimique” de Toulouse y del Departamento de Química de la Michigan State University y ha sido posible gracias a un proyecto financiado por la “Agence National pour la Recherce” y al programa PERMEANT entre el CNRS y la NSF.

A comparative analysis by means of quantum molecular similarity measures of density distributions derived from conventional ab initio and density functional methods

A procedure based on quantum molecular similarity measures (QMSM) has been used to compare electron densities obtained from conventional ab initio and density functional methodologies at their respective optimized geometries. This method has been applied to a series of small molecules which have experimentally known properties and molecular bonds of diverse degrees of ionicity and covalency. Results show that in most cases the electron densities obtained from density functional methodologies are of a similar quality than post-Hartree-Fock generalized densities. For molecules where Hartree-Fock methodology yields erroneous results, the density functional methodology is shown to yield usually more accurate densities than those provided by the second order Møller-Plesset perturbation theory

Estimation of the viscoelastic properties of vessel walls using a computational model and Doppler ultrasound

Human arteries affected by atherosclerosis are characterized by altered wall viscoelastic properties. The possibility of noninvasively assessing arterial viscoelasticity in vivo would significantly contribute to the early diagnosis and prevention of this disease. This paper presents a noniterative technique to estimate the viscoelastic parameters of a vascular wall Zener model. The approach requires the simultaneous measurement of flow variations and wall displacements, which can be provided by suitable ultrasound Doppler instruments. Viscoelastic parameters are estimated by fitting the theoretical constitutive equations to the experimental measurements using an ARMA parameter approach. The accuracy and sensitivity of the proposed method are tested using reference data generated by numerical simulations of arterial pulsation in which the physiological conditions and the viscoelastic parameters of the model can be suitably varied. The estimated values quantitatively agree with the reference values, showing that the only parameter affected by changing the physiological conditions is viscosity, whose relative error was about 27% even when a poor signal-to-noise ratio is simulated. Finally, the feasibility of the method is illustrated through three measurements made at different flow regimes on a cylindrical vessel phantom, yielding a parameter mean estimation error of 25%.

A reflection about the social and technological aspects in flood risk management - the case of the Italian Civil Protection

The right of a person to be protected from natural hazards is a characteristic of the social and economical development of the society. This paper is a contribution to the reflection about the role of Civil Protection organizations in a modern society. The paper is based in the inaugural conference made by the authors on the 9th Plinius Conference on Mediterranean Storms. Two major issues are considered. The first one is sociological; the Civil Protection organizations and the responsible administration of the land use planning should be perceived as reliable as possible, in order to get consensus on the restrictions they pose, temporary or definitely, on the individual free use of the territory as well as in the entire warning system. The second one is technological: in order to be reliable they have to issue timely alert and warning to the population at large, but such alarms should be as "true" as possible. With this aim, the paper summarizes the historical evolution of the risk assessment, starting from the original concept of "hazard", introducing the concepts of "scenario of event" and "scenario of risk" and ending with a discussion about the uncertainties and limits of the most advanced and efficient tools to predict, to forecast and to observe the ground effects affecting people and their properties. The discussion is centred in the case of heavy rains and flood events in the North-West of Mediterranean Region.

Structural and functional characterization of (110)-oriented epitaxial La2/3Ca1/3MnO3 electrodes and SrTiO3 tunnel barriers

La2/3Ca1/3MnO3 (LCMO) films have been deposited on (110)-oriented SrTiO3 (STO) substrates. X-ray diffraction and high-resolution electron microscopy reveal that the (110) LCMO films are epitaxial and anisotropically in-plane strained, with higher relaxation along the [1¿10] direction than along the [001] direction; x-ray absorption spectroscopy data signaled the existence of a single intermediate Mn3+/4+ 3d-state at the film surface. Their magnetic properties are compared to those of (001) LCMO films grown simultaneously on (001) STO substrates It is found that (110) LCMO films present a higher Curie temperature (TC) and a weaker decay of magnetization when approaching TC than their (001) LCMO counterparts. These improved films have been subsequently covered by nanometric STO layers. Conducting atomic-force experiments have shown that STO layers, as thin as 0.8 nm, grown on top of the (110) LCMO electrode, display good insulating properties. We will show that the electric conductance across (110) STO layers, exponentially depending on the barrier thickness, is tunnel-like. The barrier height in STO (110) is found to be similar to that of STO (001). These results show that the (110) LCMO electrodes can be better electrodes than (001) LCMO for magnetic tunnel junctions, and that (110) STO are suitable insulating barriers.

Current-density-functional approach to large quantum dots in intense magnetic fields

Within current-density-functional theory, we have studied a quantum dot made of 210 electrons confined in a disk geometry. The ground state of this large dot exhibits some features as a function of the magnetic field (Beta) that can be attributed in a clear way to the formation of compressible and incompressible states of the system. The orbital and spin angular momenta, the total energy, ionization and electron chemical potentials of the ground state, as well as the frequencies of far-infrared edge modes are calculated as a function of Beta, and compared with available experimental and theoretical results.