Exploring unfrequent events with accelerated molecular dynamics simulations: from photochemistry to drug design

La meva incorporació al grup de recerca del Prof. McCammon (University of California San Diego) en qualitat d’investigador post doctoral amb una beca Beatriu de Pinós, va tenir lloc el passat 1 de desembre de 2010; on vaig dur a terme les meves tasques de recerca fins al darrer 1 d’abril de 2012. El Prof. McCammon és un referent mundial en l’aplicació de simulacions de dinàmica molecular (MD) en sistemes biològics d’interès humà. La contribució més important del Prof. McCammon en la simulació de sistemes biològics és el desenvolupament del mètode de dinàmiques moleculars accelerades (AMD). Les simulacions MD convencionals, les quals estan limitades a l’escala de temps del nanosegon (~10-9s), no son adients per l’estudi de sistemes biològics rellevants a escales de temps mes llargues (μs, ms...). AMD permet explorar fenòmens moleculars poc freqüents però que son clau per l’enteniment de molts sistemes biològics; fenòmens que no podrien ser observats d’un altre manera. Durant la meva estada a la “University of California San Diego”, vaig treballar en diferent aplicacions de les simulacions AMD, incloent fotoquímica i disseny de fàrmacs per ordinador. Concretament, primer vaig desenvolupar amb èxit una combinació dels mètodes AMD i simulacions Car-Parrinello per millorar l’exploració de camins de desactivació (interseccions còniques) en reaccions químiques fotoactivades. En segon lloc, vaig aplicar tècniques estadístiques (Replica Exchange) amb AMD en la descripció d’interaccions proteïna-lligand. Finalment, vaig dur a terme un estudi de disseny de fàrmacs per ordinador en la proteïna-G Rho (involucrada en el desenvolupament de càncer humà) combinant anàlisis estructurals i simulacions AMD. Els projectes en els quals he participat han estat publicats (o estan encara en procés de revisió) en diferents revistes científiques, i han estat presentats en diferents congressos internacionals. La memòria inclosa a continuació conté més detalls de cada projecte esmentat.

UBVRI photoelectric photometry of nearby stars

In order to complete the photometric data of the Gliese (1969) 'Catalog of Nearby Stars', and in addition use these data for the Hipparcos space astrometry mission, program stars have been selected from the catalog and its supplements on the basis of their having an incomplete set of UBVRI photometric data of magnitude lower than 13. The program developed rejects determinations of any magnitude or color index having a residual greater than 2(sigma-prime), where sigma-prime is the standard deviation for the determinations of unit weight.

INTEGRAL and XMM-Newton observations towards the unidentified MeV source GRO J1411-64.

The COMPTEL unidentified source GRO J1411-64 was observed by INTEGRAL, and its central part, also by XMM-Newton. The data analysis shows no hint for new detections at hard X-rays. The upper limits in flux herein presented constrain the energy spectrum of whatever was producing GRO J1411-64, imposing, in the framework of earlier COMPTEL observations, the existence of a peak in power output located somewhere between 300-700 keV for the so-called low state. The Circinus Galaxy is the only source detected within the 4$\sigma$ location error of GRO J1411-64, but can be safely excluded as the possible counterpart: the extrapolation of the energy spectrum is well below the one for GRO J1411-64 at MeV energies. 22 significant sources (likelihood $> 10$) were extracted and analyzed from XMM-Newton data. Only one of these sources, XMMU J141255.6-635932, is spectrally compatible with GRO J1411-64 although the fact the soft X-ray observations do not cover the full extent of the COMPTEL source position uncertainty make an association hard to quantify and thus risky. The unique peak of the power output at high energies (hard X-rays and gamma-rays) resembles that found in the SED seen in blazars or microquasars. However, an analysis using a microquasar model consisting on a magnetized conical jet filled with relativistic electrons which radiate through synchrotron and inverse Compton scattering with star, disk, corona and synchrotron photons shows that it is hard to comply with all observational constrains. This and the non-detection at hard X-rays introduce an a-posteriori question mark upon the physical reality of this source, which is discussed in some detail.

Myosin motors and not actin comets are mediators of the actin-based Golgi-to-endoplasmic reticulum protein transport

We have previously reported that actin filaments are involved in protein transport from the Golgi complex to the endoplasmic reticulum. Herein, we examined whether myosin motors or actin comets mediate this transport. To address this issue we have used, on one hand, a combination of specific inhibitors such as 2,3-butanedione monoxime (BDM) and 1-[5-isoquinoline sulfonyl]-2-methyl piperazine (ML7), which inhibit myosin and the phosphorylation of myosin II by the myosin light chain kinase, respectively; and a mutant of the nonmuscle myosin II regulatory light chain, which cannot be phosphorylated (MRLC2AA). On the other hand, actin comet tails were induced by the overexpression of phosphatidylinositol phosphate 5-kinase. Cells treated with BDM/ML7 or those that express the MRLC2AA mutant revealed a significant reduction in the brefeldin A (BFA)-induced fusion of Golgi enzymes with the endoplasmic reticulum (ER). This delay was not caused by an alteration in the formation of the BFA-induced tubules from the Golgi complex. In addition, the Shiga toxin fragment B transport from the Golgi complex to the ER was also altered. This impairment in the retrograde protein transport was not due to depletion of intracellular calcium stores or to the activation of Rho kinase. Neither the reassembly of the Golgi complex after BFA removal nor VSV-G transport from ER to the Golgi was altered in cells treated with BDM/ML7 or expressing MRLC2AA. Finally, transport carriers containing Shiga toxin did not move into the cytosol at the tips of comet tails of polymerizing actin. Collectively, the results indicate that 1) myosin motors move to transport carriers from the Golgi complex to the ER along actin filaments; 2) nonmuscle myosin II mediates in this process; and 3) actin comets are not involved in retrograde transport.

Thrombin-induced contraction in alveolar epithelial cells probed by traction microscopy

Contractile tension of alveolar epithelial cells plays a major role in the force balance that regulates the structural integrity of the alveolar barrier. The aim of this work was to study thrombin-induced contractile forces of alveolar epithelial cells. A549 alveolar epithelial cells were challenged with thrombin, and time course of contractile forces was measured by traction microscopy. The cells exhibited basal contraction with total force magnitude 55.0 ± 12.0 nN (mean ± SE, n = 12). Traction forces were exerted predominantly at the cell periphery and pointed to the cell center. Thrombin (1 U/ml) induced a fast and sustained 2.5-fold increase in traction forces, which maintained peripheral and centripetal distribution. Actin fluorescent staining revealed F-actin polymerization and enhancement of peripheral actin rim. Disruption of actin cytoskeleton with cytochalasin D (5 µM, 30 min) and inhibition of myosin light chain kinase with ML-7 (10 µM, 30 min) and Rho kinase with Y-27632 (10 µM, 30 min) markedly depressed basal contractile tone and abolished thrombin-induced cell contraction. Therefore, the contractile response of alveolar epithelial cells to the inflammatory agonist thrombin was mediated by actin cytoskeleton remodeling and actomyosin activation through myosin light chain kinase and Rho kinase signaling pathways. Thrombin-induced contractile tension might further impair alveolar epithelial barrier integrity in the injured lung.

Supertubes

It is shown that a IIA superstring carrying D0-brane charge can be "blown up", in a Minkowski vacuum background, to a (1/4)-supersymmetric tubular D2-brane, supported against collapse by the angular momentum generated by crossed electric and magnetic Born-Infeld fields. This supertube can be viewed as a world-volume realization of the sigma-model Q lump.

Análisis de convergencia de las regiones de la zona euro (1990-2010)

Since the birth of Economic and Monetary Union (EMU), policies have been implemented in the Member States of the European Union (EU) to lead them towards economic convergence. This article analyses the convergence of the 174 regions that exist in the 17 euro-zone countries in the years from 1990 to 2010. The article specifies a space-time econometric model using the hypotheses of conditioned beta-convergence and sigmaconvergence. The dependent variables of the model are per capita GDP and productivity and the explanatory variables are real economic variables. Beta-convergence is found to exist between the countries of the euro-zone in terms of per capita GDP, but there is divergence in terms of productivity, though only at country level. In other words, the hypothesis is confirmed that it is guidelines at country level that lead to hypothetical convergence and that the unfavourable performance of productivity is due, without doubt, to differences in behaviour between the active populations of the different euro zone countries

La paulatina incorporación del estándar CERIF al diseño de sistemas integrados de gestión científica

Núria Cuní y Juan Pedro Belchi, representantes del Consorcio Sigma Gestión Universitaria, miembro institucional de euroCRIS, hablaron de sus previsiones para la incorporación de CERIF al desarrollo de su módulo Argos para sistemas CRIS universitarios, previa descripción de la aplicación de Argos a la integración de diversos sistemas institucionales en la Universitat Pompeu Fabra. El trabajo de implantación de Argos en la UPF incluyó la puesta a punto del estándar CVN, y en la presentación se relacionó dicho proyecto CVN con la adaptación progresiva del modelo de datos de Argos hacia CERIF.

Rainfall is a risk factor for sporadic cases of Legionella pneumophila Pneumonia

It is not known whether rainfall increases the risk of sporadic cases of Legionella pneumonia. We sought to test this hypothesis in a prospective observational cohort study of non-immunosuppressed adults hospitalized for community-acquired pneumonia (1995-2011). Cases with Legionella pneumonia were compared with those with non-Legionella pneumonia. Using daily rainfall data obtained from the regional meteorological service we examined patterns of rainfall over the days prior to admission in each study group. Of 4168 patients, 231 (5.5%) had Legionella pneumonia. The diagnosis was based on one or more of the following: sputum (41 cases), antigenuria (206) and serology (98). Daily rainfall average was 0.556 liters/m2 in the Legionella pneumonia group vs. 0.328 liters/m2 for non-Legionella pneumonia cases (p = 0.04). A ROC curve was plotted to compare the incidence of Legionella pneumonia and the weighted median rainfall. The cut-off point was 0.42 (AUC 0.54). Patients who were admitted to hospital with a prior weighted median rainfall higher than 0.42 were more likely to have Legionella pneumonia (OR 1.35; 95% CI 1.02-1.78; p = .03). Spearman Rho correlations revealed a relationship between Legionella pneumonia and rainfall average during each two-week reporting period (0.14; p = 0.003). No relationship was found between rainfall average and non-Legionella pneumonia cases (−0.06; p = 0.24). As a conclusion, rainfall is a significant risk factor for sporadic Legionella pneumonia. Physicians should carefully consider Legionella pneumonia when selecting diagnostic tests and antimicrobial therapy for patients presenting with CAP after periods of rainfall.

Variaciones dimensionales en piezas plásticas de inyección y análisis de los medios de control

En la industria de la automoción, así como en todas las que se dedican a fabricar piezas, ya sean plásticas o de otros materiales, es tan importante la Producción como la Calidad. No sirve de nada fabricar mucho si no son piezas de una calidad adecuada, y del mismo modo no es rentable fabricar muy poco volumen por mucho que tenga una calidad excelente. Por ello hay que buscar siempre el equilibrio entre ambos conceptos. La finalidad es tener procesos lo más robustos posibles que nos permitan fabricar cantidad con una buena calidad. La finalidad de este trabajo es buscar los parámetros que más afectan en un proceso de inyección, es decir, saber cuáles son los que debemos tener bajo control para lograr una calidad de piezas buena y un proceso estable y controlado. Para ver si el proceso es capaz de lograr ese objetivo utilizamos gráficos basados en la teoría de 6- sigma que nos calculan el coeficiente de capacidad del proceso (Cpk). A su vez analizaremos los sistemas de medida que utilizamos en cada una de las piezas analizadas para evaluar si son los correctos y nos permiten discriminar piezas buenas de malas en el proceso productivo. La conclusión del trabajo es que hay que prestar especial atención en controlar aquellos aspectos de un proceso que nos aportan variación, y no invertir tiempo ni dinero en aquellos otros que no nos aportan valor añadido y que no afectan sustancialmente al proceso. Este análisis por supuesto lleva su coste, que he analizado y plasmado en las conclusiones para saber lo que le cuesta aproximadamente a una empresa realizarlo.

Economic and social convergence in Colombia

GDP has usually been used as a proxy for human well-being. Nevertheless, other social aspects should also be considered, such as life expectancy, infant mortality, educational enrolment and crime issues. With this paper we investigate not only economic convergence but also social convergence between regions in a developing country, Colombia, in the period 1975-2005. We consider several techniques in our analysis: sigma convergence, stochastic kernel estimations, and also several empirical models to find out the beta convergence parameter (cross section and panel estimates, with and without spatial dependence). The main results confirm that we can talk about convergence in Colombia in key social variables, although not in the classic economic variable, GDP per capita. We have also found that spatial autocorrelation reinforces convergence processes through deepening market and social factors, while isolation condemns regions to nonconvergence.

The use of cost per life year gained as a measurement of cost-effectiveness in Spain: a systematic review of recent publications

The objective of this study was to evaluate the methodological characteristics of cost-effectiveness evaluations carried out in Spain, since 1990, which include LYG as an outcome to measure the incremental cost-effectiveness ratio. METHODS: A systematic review of published studies was conducted describing their characteristics and methodological quality. We analyse the cost per LYG results in relation with a commonly accepted Spanish cost-effectiveness threshold and the possible relation with the cost per quality adjusted life year (QALY) gained when they both were calculated for the same economic evaluation. RESULTS: A total of 62 economic evaluations fulfilled the selection criteria, 24 of them including the cost per QALY gained result as well. The methodological quality of the studies was good (55%) or very good (26%). A total of 124 cost per LYG results were obtained with a mean ratio of 49,529 and a median of 11,490 (standard deviation of 183,080). Since 2003, a commonly accepted Spanish threshold has been referenced by 66% of studies. A significant correlation was found between the cost per LYG and cost per QALY gained results (0.89 Spearman-Rho, 0.91 Pearson). CONCLUSIONS: There is an increasing interest for economic health care evaluations in Spain, and the quality of the studies is also improving. Although a commonly accepted threshold exists, further information is needed for decision-making as well as to identify the relationship between the costs per LYG and per QALY gained.

Terutroban, A TP-receptor antagonist, reduces portal pressure in cirrhotic rats.

Increased production of vasoconstrictive prostanoids, such as thromboxane A2 (TXA2 ), contributes to endothelial dysfunction and increased hepatic vascular tone in cirrhosis. TXA2 induces vasoconstriction by way of activation of the thromboxane-A2 /prostaglandin-endoperoxide (TP) receptor. This study investigated whether terutroban, a specific TP receptor blocker, decreases hepatic vascular tone and portal pressure in rats with cirrhosis due to carbon tetrachloride (CCl4 ) or bile duct ligation (BDL). Hepatic and systemic hemodynamics, endothelial dysfunction, liver fibrosis, hepatic Rho-kinase activity (a marker of hepatic stellate cell contraction), and the endothelial nitric oxide synthase (eNOS) signaling pathway were measured in CCl4 and BDL cirrhotic rats treated with terutroban (30 mg/kg/day) or its vehicle for 2 weeks. Terutroban reduced portal pressure in both models without producing significant changes in portal blood flow, suggesting a reduction in hepatic vascular resistance. Terutroban did not significantly change arterial pressure in CCl4 -cirrhotic rats but decreased it significantly in BDL-cirrhotic rats. In livers from CCl4 and BDL-cirrhotic terutroban-treated rats, endothelial dysfunction was improved and Rho-kinase activity was significantly reduced. In CCl4 -cirrhotic rats, terutroban reduced liver fibrosis and decreased alpha smooth muscle actin (α-SMA), collagen-I, and transforming growth factor beta messenger RNA (mRNA) expression without significant changes in the eNOS pathway. In contrast, no change in liver fibrosis was observed in BDL-cirrhotic rats but an increase in the eNOS pathway. CONCLUSION: Our data indicate that TP-receptor blockade with terutroban decreases portal pressure in cirrhosis. This effect is due to decreased hepatic resistance, which in CCl4 -cirrhotic rats was linked to decreased hepatic fibrosis, but not in BDL rats, in which the main mediator appeared to be an enhanced eNOS-dependent vasodilatation, which was not liver-selective, as it was associated with decreased arterial pressure. The potential use of terutroban for portal hypertension requires further investigation.

La força pot predir el rendiment i la lesionabilitat al bàsquet professional?

Amb l’objectiu de conèixer les relacions existents entre la força, el rendiment esportiu i la lesionabilitat en un equip masculí de bàsquet professional, es realitza un estudi prospectiu, observacional i descriptiu d’anàlisis d’estadístiques (71 partits), test de mig esquat (n = 7) i patologia lesional, monitoritzant la temporada 09/10, on es relacionen les dades obtingudes de cada jugador referents al rendiment esportiu per partit (valoració estadística), les mitjanes de força, velocitat i potència de cada mesocicle i la lesionabilitat. La tècnica estadística utilitzada ha estat la correlació a partir del paràmetre rho de Spearman. Aquestes correlacions entre força i lesionabilitat mostren que a valors de força més elevats hi ha més lesions: amb 80 kg són molt significatives per a lesions totals (LT) i potència (rho = 0,898; p = 0,006), i significatives per força (rho = 0,823; p = 0,023) i velocitat (rho = 0,774; p = 0,041); la velocitat amb 90 kg es relaciona amb lesions time loss (TL) (rho = 0,878; p = 0,009), i la potència amb 100 kg, amb lesions totals (LT) (rho = 0,805; p = 0,029) i V100 (rho = 0,898; p = 0,006) molt significativament. I la relació entre força i rendiment és significativament negativa en 5 dels 7 mesocicles, és a dir, a menys força, més rendiment. En conclusió, durant l’execució del mig esquat, hi ha valors de força adients per rendir millor i lesionar-se menys: de 800 N a 1.050 N i amb càrregues de 80 kg a 90 kg.