Stacking-induced fluorescence increase reveals allosteric interactions through DNA

From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye–DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids

Closed-loop compensation of charge trapping induced by ionizing radiation in MOS capacitors

The objective of this work is to explore the capability of a charge trapping control loop to continuously compensate charge induced by ionizing radiation in the dielectric of MOS capacitors. To this effect, two devices made with silicon oxide have been simultaneously irradiated with gamma radiation: one with constant voltage bias, and the other working under a dielectric charge control. The experiment shows substantial charge trapping in the uncontrolled device whereas, at the same time, the control loop is able to compensate the charge induced by gamma radiation in the second device.Peer ReviewedPostprint (author's final draft

Integrating the goal and business process perspectives in information system analysis

There are several motivations to promote investment and scientific effort in the integration of intentional and operational perspectives: organisational reengineering, continuous improvement of business processes, alignment among complementary analysis perspectives, information traceability, etc. In this paper we propose the integration of two modelling languages that support the creation of goal and business process models: the i* goal-oriented modelling method and Communication Analysis, a communication-oriented business process modelling method. We describe the methodological integration of the two modelling methods with the aim of fulfilling several criteria: i) to rely on appropriate theories; ii) to provide abstract and concrete syntaxes; iii) to provide scenarios of application; and iv) to develop tool support. We provide guidelines for using the two modelling methods in a top-down analysis scenario. We also present an illustrative case that demonstrates the feasibility of the approach.Peer ReviewedPostprint (author's final draft

Cosmological measurement of neutrino mass in the presence of leptonic asymmetry

We show that even the smallest neutrino mass consistent with the Super--Kamiokande data is relevant for cosmological models of structure formation and cosmic microwave background (CMB) anisotropies, provided that a relic neutrino asymmetry exists. We calculate the precision with which a 0.07 eV neutrino mass could be extracted from CMB anisotropy and large-scale structure data by the future Planck satellite and Sloan Digital Sky Survey. We find that such a mass can be detected, assuming a large relic neutrino asymmetry still allowed by current experimental data. This measurement of the absolute value of the neutrino mass would be crucial for our understanding of neutrino models.Comment: 8 pages, 2 PS figures, version to be publishe

Assessing myometrial infiltration by endometrial cancer: uterine virtual navigation with three-dimensional US

To describe and analyze the diagnostic performance of uterine virtual navigation with three-dimensional (3D) ultrasonography (US) for the assessment of the depth of myometrial infiltration by endometrial cancer. MATERIALS AND METHODS: Institutional review board approval was obtained; patients gave oral informed consent. Women with endometrial cancer were evaluated by using 3D US prior to surgical staging. A 3D volume of the whole uterus was obtained and analyzed by using software. Virtual navigation through three orthogonal planes was performed to identify the shortest myometrial tumor-free distance to serosa (TDS) by analyzing the lateral, anterior, posterior, and fundal portions of the myometrium. Myometrial infiltration was also assessed by subjective impression of an examiner. Histologic findings of myometrial infiltration and TDS measured by a pathologist were used as the reference standard. A receiver operating characteristic curve was plotted to identify the best cutoff for TDS for identifying myometrial infiltration of 50% or more. RESULTS: Ninety-six women (mean age, 61.8 years; range, 31-86 years) with endometrial cancer were included in the study. At histologic analysis, myometrial invasion was found to be less than 50% in 69 (72%) cases and 50% or more in 27 (28%) cases. TDS measured with US was positively correlated with histologically measured TDS (r = 0.649; 95% confidence interval: 0.52, 0.76). The best cutoff for US-measured TDS was 9.0 mm (sensitivity, 100%; specificity, 61%; negative predictive value, 100%; positive predictive value, 50%). Subjective impression had a sensitivity of 92.6%, a specificity of 82.3%, a negative predictive value of 96.6%, and a positive predictive value of 67.7%. CONCLUSION: Uterine virtual navigation with 3D US is a reliable method for the assessment of myometrial infiltration in patients with endometrial cancer

miR-28 regulates the germinal center reaction and blocks tumor growth in preclinical models of non-Hodgkin lymphoma

Non-Hodgkin lymphoma comprises a variety of neoplasms, many of which arise from germinal center (GC)-experienced B cells. microRNA-28 (miR-28) is a GC-specific miRNA whose expression is lost in numerous mature B-cell neoplasms. Here we show that miR-28 regulates the GC reaction in primary B cells by impairing class switch recombination and memory B and plasma cell differentiation. Deep quantitative proteomics combined with transcriptome analysis identified miR-28 targets involved in cell-cycle and B-cell receptor signaling. Accordingly, we found that miR-28 expression diminished proliferation in primary and lymphoma cells in vitro. Importantly, miR-28 reexpression in human Burkitt (BL) and diffuse large B-cell lymphoma (DLBCL) xenografts blocked tumor growth, both when delivered in viral vectors or as synthetic, clinically amenable, molecules. Further, the antitumoral effect of miR-28 is conserved in a primary murine in vivo model of BL. Thus, miR-28 replacement is uncovered as a novel therapeutic strategy for DLBCL and BL treatment.This work was supported by a Ministerio de Economia y Competitividad's research training program (Formacion de Personal Investigador [FPI]) fellowship (N.B.-I.); the Ramon y Cajal program (RYC-2009-04503) funded by the Ministerio de Educacion, Cultura y Deporte and the European Research Council Proof of Concept program (HEAL-BY-MIRNA 713728) (V.G.d.Y.); the Centro Nacional de Investigaciones Cardiovaculares (CNIC) (A.F.A.-P., S.M.M., A.R.R.); the Ministerio de Economia y Competitividad (SAF2010-21394, SAF2013-42767-R), the European Research Council Starting Grant program (BCLYM-207844), and Proof of Concept program (HEAL-BY-MIRNA 713728) (A.R.R.); the People Programme-Marie Curie Actions (FP7-PIIF-2012-328177), Spanish Ministry of Economy and Competitiveness (MINECO; SAF2013-45787-R), and Gobierno de Navarra (GN-106/2014) (S.R.); and the Ministerio de Economia y Competitividad (BIO2012-37926 and BIO2015-67580-P), Instituto de Salud Carlos III (Fondo de Investigacion Sanitaria [FIS] grants PRB2 [IPT13/0001, Proteo-Red], the Fundacion La Marato TV3, and Redes tematicas de investigacion cooperativa en salud [RETICS] [RD12/0042/00056, RIC]) (J.V.). This work has been cofunded by Fondo Europeo de Desarrollo Regional (FEDER) funds. The CNIC is supported by the and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (MINECO award SEV-2015-0505).S

Alterations in Lipid Levels of Mitochondrial Membranes Induced by Amyloid-β: A Protective Role of Melatonin

Alzheimer pathogenesis involves mitochondrial dysfunction, which is closely related to amyloid-β (Aβ) generation, abnormal tau phosphorylation, oxidative stress, and apoptosis. Alterations in membranal components, including cholesterol and fatty acids, their characteristics, disposition, and distribution along the membranes, have been studied as evidence of cell membrane alterations in AD brain. The majority of these studies have been focused on the cytoplasmic membrane; meanwhile the mitochondrial membranes have been less explored. In this work, we studied lipids and mitochondrial membranes in vivo, following intracerebral injection of fibrillar amyloid-β (Aβ). The purpose was to determine how Aβ may be responsible for beginning of a vicious cycle where oxidative stress and alterations in cholesterol, lipids and fatty acids, feed back on each other to cause mitochondrial dysfunction. We observed changes in mitochondrial membrane lipids, and fatty acids, following intracerebral injection of fibrillar Aβ in aged Wistar rats. Melatonin, a well-known antioxidant and neuroimmunomodulator indoleamine, reversed some of these alterations and protected mitochondrial membranes from obvious damage. Additionally, melatonin increased the levels of linolenic and n-3 eicosapentaenoic acid, in the same site where amyloid β was injected, favoring an endogenous anti-inflammatory pathway

Proteomic characterization of human coronary thrombus in patients with ST-segment elevation acute myocardial infarction

Acute myocardial infarction with ST-segment elevation (STEMI) initiates with intraluminal thrombosis and results in total occlusion of the coronary artery. To date, characterization of the coronary thrombus proteome in STEMI patients has not been yet accomplished. Therefore, we aimed to perform an in-depth proteomic characterization of the human coronary thrombus by means of three different approaches: 2-DE followed by mass spectrometry (MALDI MS/MS), 1-DE combined either with liquid chromatography coupled to mass spectrometry in a MALDI TOF/TOF (LC-MALDI-MS/MS), or in a LTQ-Orbitrap (LC-ESI-MS/MS). This approach allowed us to identify a total of 708 proteins in the thrombus. Expression in coronary thrombi (n=20) of 14 proteins was verified, and the expression of fibrin and 6 cell markers (platelets, monocytes, neutrophils, eosinophils, T-cells and B-cells) quantified by selected reaction monitoring (SRM). A positive correlation of 5 proteins (fermitin homolog 3, thrombospondin-1, myosin-9, beta parvin and ras-related protein Rap-1b) with CD41 was found, pointing out the potential activation of a focal adhesion pathway within thrombus platelets. DIDO1 protein was found to correlate negatively with thrombus fibrin, and was found up-regulated in the plasma of these STEMI patients, which may constitute a starting point for further analyses in the search for biomarkers of thrombosis. BIOLOGICAL SIGNIFICANCE: The proteomic characterization of the human coronary thrombus may contribute to a better understanding of the mechanisms involved in acute coronary syndrome, and thus pave the road for the identification of new therapeutic targets that may help addressing this and other thrombotic diseases. A novel methodology to characterize thrombus composition and expression of a sub-group of proteins is hereby described, which allowed linking protein expression with cellular and ECM matrix composition of the thrombus. Five proteins (fermitin homolog 3, thrombospondin-1, myosin-9, beta parvin and ras-related protein Rap-1b) co-express within the human coronary thrombus with CD41, pointing out the potential activation of a focal adhesion pathway within thrombus platelets during thrombus formation. Besides, the protein death-inducer obliterator 1, found to be expressed within the human coronary thrombus, has been proved to increase in the plasma of STEMI patients, which constitutes an important starting point for further analyses in the search for biomarkers of thrombosis.This work was supported by grants from the Instituto de Salud Carlos III (FIS PI070537, PI11/02239), Fondos Feder, Redes temáticas de Investigación Cooperativa en Salud (RD12/0042/ 0071, RD06/0014/1015), and Fundación para la Investigación Sanitaria de Castilla-La Mancha (FISCAM PI2008-08, PI2008-28, PI2008-52). These results are lined up with the Spanish initiative on the Human Proteome Project (SpHPP). The CNIC is supported by the Spanish Ministerio de Economia y Competitividad and the Fundacion Pro-CNIC. We would like to thank Dr. Gloria Alvarez-Llamas for her kind suggestions for the manuscript; Gemma Barroso from Proteomic Unit, Hospital Nacional de Paraplejicos, for her help and dedication to this work, as well as Veronica Moral and Ana Gallardo from the same Unit, and TamaraSastre andCarmenBermudez for their technical support.S