DNA Damage and Transcriptional Changes in the Gills of Mytilus galloprovincialis Exposed to Nanomolar Doses of Combined Metal Salts (Cd, Cu, Hg)

[ENG]Aiming at an integrated and mechanistic view of the early biological effects of selected metals in the marine sentinel organism Mytilus galloprovincialis, we exposed mussels for 48 hours to 50, 100 and 200 nM solutions of equimolar Cd, Cu and Hg salts and measured cytological and molecular biomarkers in parallel. Focusing on the mussel gills, first target of toxic water contaminants and actively proliferating tissue, we detected significant dose-related increases of cells with micronuclei and other nuclear abnormalities in the treated mussels, with differences in the bioconcentration of the three metals determined in the mussel flesh by atomic absorption spectrometry. Gene expression profiles, determined in the same individual gills in parallel, revealed some transcriptional changes at the 50 nM dose, and substantial increases of differentially expressed genes at the 100 and 200 nM doses, with roughly similar amounts of up- and down-regulated genes. The functional annotation of gill transcripts with consistent expression trends and significantly altered at least in one dose point disclosed the complexity of the induced cell response. The most evident transcriptional changes concerned protein synthesis and turnover, ion homeostasis, cell cycle regulation and apoptosis, and intracellular trafficking (transcript sequences denoting heat shock proteins, metal binding thioneins, sequestosome 1 and proteasome subunits, and GADD45 exemplify up-regulated genes while transcript sequences denoting actin, tubulins and the apoptosis inhibitor 1 exemplify down-regulated genes). Overall, nanomolar doses of co-occurring free metal ions have induced significant structural and functional changes in the mussel gills: the intensity of response to the stimulus measured in laboratory supports the additional validation of molecular markers of metal exposure to be used in Mussel Watch programs

The Loss of Functional Caspase-12 in Europe Is a Pre-Neolithic Event

6 p.

Early Functional Deficit and Microglial Disturbances in a Mouse Model of Amyotrophic Lateral Sclerosis

11 p.

A methodology for the semiautomatic annotation of EPEC-RolSem, a basque corpus labeled at predicative level following the PropBank-Verb Net model

In this article we describe the methodology developed for the semiautomatic annotation of EPEC-RolSem, a Basque corpus labeled at predicate level following the PropBank-VerbNet model. The methodology presented is the product of detailed theoretical study of the semantic nature of verbs in Basque and of their similarities and differences with verbs in other languages. As part of the proposed methodology, we are creating a Basque lexicon on the PropBank-VerbNet model that we have named the Basque Verb Index (BVI). Our work thus dovetails the general trend toward building lexicons from tagged corpora that is clear in work conducted for other languages. EPEC-RolSem and BVI are two important resources for the computational semantic processing of Basque; as far as the authors are aware, they are also the first resources of their kind developed for Basque. In addition, each entry in BVI is linked to the corresponding verb-entry in well-known resources like PropBank, VerbNet, WordNet, Levin’s Classification and FrameNet. We have also implemented several automatic processes to aid in creating and annotating the BVI, including processes designed to facilitate the task of manual annotation.

The study of film adaptation: a state of the art and some "new" functional proposals

Eguíluz, Federico; Merino, Raquel; Olsen, Vickie; Pajares, Eterio; Santamaría, José Miguel (eds.)

Assisting blog publication: annotation, model transformation, and crossblogging techniques

Although blogs exist from the beginning of the Internet, their use has considerablybeen increased in the last decade. Nowadays, they are ready for being used bya broad range of people. From teenagers to multinationals, everyone can have aglobal communication space.Companies know blogs are a valuable publicity tool to share information withthe participants, and the importance of creating consumer communities aroundthem: participants come together to exchange ideas, review and recommend newproducts, and even support each other. Also, companies can use blogs for differentpurposes, such as a content management system to manage the content of websites,a bulletin board to support communication and document sharing in teams,an instrument in marketing to communicate with Internet users, or a KnowledgeManagement Tool. However, an increasing number of blog content do not findtheir source in the personal experiences of the writer. Thus, the information cancurrently be kept in the user¿s desktop documents, in the companies¿ catalogues,or in another blogs. Although the gap between blog and data source can be manuallytraversed in a manual coding, this is a cumbersome task that defeats the blog¿seasiness principle. Moreover, depending on the quantity of information and itscharacterisation (i.e., structured content, unstructured content, etc.), an automaticapproach can be more effective.Based on these observations, the aim of this dissertation is to assist blog publicationthrough annotation, model transformation and crossblogging techniques.These techniques have been implemented to give rise to Blogouse, Catablog, andBlogUnion. These tools strive to improve the publication process considering theaforementioned data sources.

Fine mapping and functional analysis of the multiple sclerosis risk gene CD6

CD6 has recently been identified and validated as risk gene for multiple sclerosis (MS), based on the association of a single nucleotide polymorphism (SNP), rs17824933, located in intron 1. CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation. In this study, we performed a haptag SNP screen of the CD6 gene locus using a total of thirteen tagging SNPs, of which three were non-synonymous SNPs, and replicated the recently reported GWAS SNP rs650258 in a Spanish-Basque collection of 814 controls and 823 cases. Validation of the six most strongly associated SNPs was performed in an independent collection of 2265 MS patients and 2600 healthy controls. We identified association of haplotypes composed of two non-synonymous SNPs [rs11230563 (R225W) and rs2074225 (A257V)] in the 2nd SRCR domain with susceptibility to MS (Pmax(T) permutation=161024). The effect of these haplotypes on CD6 surface expression and cytokine secretion was also tested. The analysis showed significantly different CD6 expression patterns in the distinct cell subsets, i.e. – CD4+ naı¨ve cells, P = 0.0001; CD8+ naı¨ve cells, P,0.0001; CD4+ and CD8+ central memory cells, P = 0.01 and 0.05, respectively; and natural killer T (NKT) cells, P = 0.02; with the protective haplotype (RA) showing higher expression of CD6. However, no significant changes were observed in natural killer (NK) cells, effector memory and terminally differentiated effector memory T cells. Our findings reveal that this new MS-associated CD6 risk haplotype significantly modifies expression of CD6 on CD4+ and CD8+ T cells.

Functional analysis of cancer-associated EGFR mutants using a cellular assay with YFP-tagged EGFR intracellular domain

Background: The presence of EGFR kinase domain mutations in a subset of NSCLC patients correlates with the response to treatment with the EGFR tyrosine kinase inhibitors gefitinib and erlotinib. Although most EGFR mutations detected are short deletions in exon 19 or the L858R point mutation in exon 21, more than 75 different EGFR kinase domain residues have been reported to be altered in NSCLC patients. The phenotypical consequences of different EGFR mutations may vary dramatically, but the majority of uncommon EGFR mutations have never been functionally evaluated. Results: We demonstrate that the relative kinase activity and erlotinib sensitivity of different EGFR mutants can be readily evaluated using transfection of an YFP-tagged fragment of the EGFR intracellular domain (YFP-EGFR-ICD), followed by immunofluorescence microscopy analysis. Using this assay, we show that the exon 20 insertions Ins770SVD and Ins774HV confer increased kinase activity, but no erlotinib sensitivity. We also show that, in contrast to the common L858R mutation, the uncommon exon 21 point mutations P848L and A859T appear to behave like functionally silent polymorphisms. Conclusion: The ability to rapidly obtain functional information on EGFR variants of unknown relevance using the YFP-EGFR-ICD assay might prove important in the future for the management of NSCLC patients bearing uncommon EGFR mutations. In addition, our assay may be used to determine the response of resistant EGFR mutants to novel second-generation TKIs.

Annotation of orthologous genes in Tunnus thynnus and T.albacore species

Albacore and Atlantic Bluefin tuna are two pelagic fish. Atlantic Bluefin tuna is included in the IUCN red list of threatened species and albacore is considered to be near threatened, so conservation plans are needed. However, no genomic resources are available for any of them. In this study, to better understand their transcriptome we functionally annotated orthologous genes. In all, 159 SNPs distributed in 120 contigs of the muscle transcriptome were analyzed. Genes were predicted for 98 contigs (81.2%) using the bioinformatics tool BLAST. In addition, another bioinformatics tool, BLAST2GO was used in order to achieve GO terms for the genes, in which 41 sequences were given a biological process, and 39 sequences were given a molecular process. The most repeated biological process was metabolism and it is important that no cellular process was given in any of the sequences. The most abundant molecular process was binding and very few catalytic activity processes were given. From the initial 159 SNPs, 40 were aligned with a sequence in the database after BLAST2GO was run, and were polymorphic in Atlantic Bluefin tuna and monomorphic in albacore. From these 40 SNPs, 24 were located in an open reading frame of which four were non-synonymous and 20 were synonymous and 16 were not located in a known open reading frame,. This study provides information for better understanding the ecology and evolution of these species and this is important in order to establish a proper conservation plan and an appropriate management.

DEVELOPMENT AND APPLICATIONS OF TIME-DEPENDENT DENSITY MATRIX FUNCTIONAL THEORY

En esta tesis estudiamos las teorías sobre la Matriz Densidad Reducida (MDR) como un marco prometedor. Nos enfocamos sobre esta teorías desde dos aspectos: Primero, usamos algunos modelos sencillos hechos con dos partículas las cuales estan armónicamente confinadas como una base para ilustrar la utilidad de la matriz densidad. Para tales sistemas, usamos la MDR de un cuerpo para calcular algunas cantidades de interés tales como densidad de momentum. Posteriormente obtenemos los orbitales naturales y su número de ocupación para algunos de los modelos, y en uno de los casos expresamos la MDR de dos cuerpos de manera exacta en términos de la MDR de un cuerpo. También usamos el teorema diferencial del virial para establecer una descripción unificada de la familia entera de estos sistemas modelo en términos de la densidad. En la seguna parte cambiamos a casos fuera del equilibrio y analizamos la así llamada jerarquía BBGKY de ecuaciones para describir la evolución temporal de un sistema de muchos cuerpos en términos de sus MDRs (a todos los órdenes). Proveemos un exhaustivo estudio de los desafíos y problemas abiertos ligados a la truncación de tales jerarquías de ecuaciones para hacerlas aplicables. Restringimos nuestro análisis a la evolución acoplada de la MDR de uno y dos cuerpos, donde los efectos de correlación de alto orden estan embebidos dentro de la aproximación usada para cerrar las ecuaciones. Probamos que dentro de esta aproximación, el número de electrones y la energía total se conservan, sin importar la aproximación usada. Luego, demostramos que aplicando los esquemas de truncación de estado base para llevar los electrones a comportamientos indeseables y no físicos, tales como la violación e incluso la divergencia en la densidad electrónica local, tanto en regímenes correlacionados débiles y fuertes.

Specific Interaction with Cardiolipin Triggers Functional Activation of Dynamin-Related Protein 1

Dynamin-Related Protein 1 (Drp1), a large GTPase of the dynamin superfamily, is required for mitochondrial fission in healthy and apoptotic cells. Drp1 activation is a complex process that involves translocation from the cytosol to the mitochondrial outer membrane (MOM) and assembly into rings/spirals at the MOM, leading to membrane constriction/division. Similar to dynamins, Drp1 contains GTPase (G), bundle signaling element (BSE) and stalk domains. However, instead of the lipid-interacting Pleckstrin Homology (PH) domain present in the dynamins, Drp1 contains the so-called B insert or variable domain that has been suggested to play an important role in Drp1 regulation. Different proteins have been implicated in Drp1 recruitment to the MOM, although how MOM-localized Drp1 acquires its fully functional status remains poorly understood. We found that Drp1 can interact with pure lipid bilayers enriched in the mitochondrion-specific phospholipid cardiolipin (CL). Building on our previous study, we now explore the specificity and functional consequences of this interaction. We show that a four lysine module located within the B insert of Drp1 interacts preferentially with CL over other anionic lipids. This interaction dramatically enhances Drp1 oligomerization and assembly-stimulated GTP hydrolysis. Our results add significantly to a growing body of evidence indicating that CL is an important regulator of many essential mitochondrial functions.

Density-potential mapping in the standard and quantum electrodynamical time-dependent density functional theory

131 p.

Hyers-Ulam-Rassias Stability of Functional Differential Systems with Point and Distributed Delays

This paper investigates stability and asymptotic properties of the error with respect to its nominal version of a nonlinear time-varying perturbed functional differential system subject to point, finite-distributed, and Volterra-type distributed delays associated with linear dynamics together with a class of nonlinear delayed dynamics. The boundedness of the error and its asymptotic convergence to zero are investigated with the results being obtained based on the Hyers-Ulam-Rassias analysis.

Interaction between the 5-HT system and the basal ganglia: functional implication and therapeutic perspective in Parkinson's disease

The neurotransmitter serotonin (5-HT) has a multifaceted function in the modulation of information processing through the activation of multiple receptor families, including G-protein-coupled receptor subtypes (5-HT1, 5-HT2, 5-HT4-7) and ligand-gated ion channels (5-HT3). The largest population of serotonergic neurons is located in the midbrain, specifically in the raphe nuclei. Although the medial and dorsal raphe nucleus (DRN) share common projecting areas, in the basal ganglia (BG) nuclei serotonergic innervations come mainly from the DRN. The BG are a highly organized network of subcortical nuclei composed of the striatum (caudate and putamen), subthalamic nucleus (STN), internal and external globus pallidus (or entopeduncular nucleus in rodents, GPi/EP and GPe) and substantia nigra (pars compacta, SNc, and pars reticulata, SNr). The BG are part of the cortico-BG-thalamic circuits, which play a role in many functions like motor control, emotion, and cognition and are critically involved in diseases such as Parkinson's disease (PD). This review provides an overview of serotonergic modulation of the BG at the functional level and a discussion of how this interaction may be relevant to treating PD and the motor complications induced by chronic treatment with L-DOPA.

Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.