Estudis funcionals i de plegament dels dominis d'activació de les procarboxipeptidases

Els dominis d’activació (ADs) de les procarboxipeptidases de la subfamília A/B sempre han sorprès ja que representen una quarta part del proenzim. S’han realitzat alguns estudis per intentar descobrir-ne alguna possible funció alternativa, però no han estat fructífers. El descobriment de l’elevada velocitat de plegament del domini d’activació de la procarboxipeptidasa A2 humana, (ADA2h), emperò, va portar a proposar la possibilitat de que realitzessin una funció d’assistència al plegament del domini enzimàtic. Posteriorment, l’anàlisi del plegament d’ADA2h a pH baix va revelar la capacitat d’aquest domini per formar fibres amiloides, a més de demostrar que un increment de l’estabilitat proteica podia prevenir la formació d’aquests agregats. La profunda caracterització del plegament d’ADA2h va fer que aquesta proteïna fos un bon model amiloidogènic, de manera que es van proposar un seguit d’experiments que s’han desenvolupat en el present treball per tal de conèixer millor aquest procés. S’han dut a terme estudis cinètics d’agregació per tal de valorar la contribució dels diferents aminoàcids de la seqüència polipeptídica, utilitzant 29 variants puntuals d’ADA2h. Es va eliminar la contribució de l’estabilitat mitjançant la utilització d’urea, i per dicroïsme circular conjuntament amb un aparell de flux detingut, es van obtenir dues velocitats diferents, v1 i v2, que corresponen a la formació d’un intermediari i a la seva reorganització, respectivament. Experiments complementaris utilitzant espectroscòpia d’infraroig (IR) revelaren la reorganització de l’estat natiu (en aquest cas) per a donar la forma agregada. Les cinètiques d’IR van mostrar que ADA2h forma l’estructura _ típica de les fibres amiloides, previ desplegament les seves hèlixs-_. Finalment, s’han realitzat estudis de biocomputació per tal d’esbrinar possibles funcions alternatives dels ADs. Les superposicions estructurals semblen mostrar similaritat dels ADs amb dominis de reconeixement d’RNA (RRM). Aquesta hipòtesi s’ha comprovat experimentalment amb ADA4h, mostrant una dèbil, però existent, unió a RNA.

gvSIG en España Virtual

España Virtual es un proyecto de I+D, subvencionado por el [CDTI] dentro del programa Ingenio 2010, orientado a la definición de la arquitectura, protocolos y estándares de la futura Internet 3D, con un foco especial en lo relativo a visualización 3D, inmersión en mundos virtuales, interacción entre usuarios y a la introducción de aspectos semánticos, sin dejar de lado el estudio y maduración de las tecnologías para el procesamiento masivo y almacenamiento de datos geográficos. Con una duración de cuatro años, el proyecto está liderado por Elecnor DEIMOS y cuenta con la participación del Centro Nacional de Información Geográfica (IGN/CNIG), Indra Espacio, Androme Ibérica, GeoSpatiumLab, DNX, [Prodevelop], Telefónica I+D y una decena de prestigiosos centros de investigación y universidades nacionales. En este contexto Prodevelop y el Ai2 (Instituto de Automática e Informática Industrial) entran a participar en el proyecto gracias a la Asociación gvSIG con el objetivo de impulsar el desarrollo de la visualización 3D , incorporación de nuevos estándares y mejoras en los ya existentes, así como la evolución de funcionalidades, sobre todo en el ámbito de los servicios remotos y mejoras del rendimiento a través de sistemas de cacheado de datos. También se pretende servir como plataforma para el volcado de resultados en los diferentes activos experimentales realizados por otros socios del proyecto. Para la consecución de objetivos se definen diferentes paquetes de trabajo que va a trabajar sobre nuevos tipos de datos, acceso a datos 3D multirresolución, integración de datos geográficos al vuelo, componentes de visualización 2D, 3D y 4D, algoritmia multirresolución y efectos audiovisuales inmersivos. Concretamente y dentro de estos paquetes de trabajo se presentarán los avances realizados e integrados dentro de gvSIG Desktop v2.0, y otras funcionalidades gvSIG sobre dispositivos móviles

Treball Final de Master - Servidor de Comunicacions Unificades

L'objectiu d'aquest projecte és la creació d'una prova de concepte de comunicacions unificades utilitzant productes de programari lliure existents. Aquesta prova de concepte servirà per poder fer demostracions del funcionament general del programari implicat amb el mínim de preparacions, instal·lacions i configuracions prèvies possibles. El projecte es dividirà en dos appliances o LiveCD, creats a traves de Suse Studio, anomenats Comunicacions Unificades i Comunicacions Unificades 2.Els productes de programari lliure que composen el Servidor de Comunicacions Unificades els podem classificar en productes principals, plugins o addons dels productes i productes secundaris.Com a productes principals tenim els següents servidors que cobreixen les necessitats principals del Servidor de Comunicacions Unificades:Asterisk v1.8.3 : Servidor de telefonia amb veu sobre IP (VoIP).FreePBX v2.9.0beta2 : GUI de control i administració d'Asterisk.Openfire v3.7.0 : Servidor de IM basat en el protocol XMPP.BigBlueButton v0.71a : Sistema de conferència web. Pendent finalitzar-ne l'implementació.I els seguents productes principals que cobreixen les necessitats del servidor de Comunicacions Unificades 2:Zimbra v7.0.1 : Servidor de correu electrònic i de calendari. Pendent resoldre conflicte inicialització LDAP.Funambol v9.0.0 : Sincronització Zimbra amb mòbils.Com a plugins o addons del productes tenim, classificats segons el producte:Asterisk addons: chan_jingle i chan_gtalkZimlets: Asterisk, Google Translator, Funambol i SocialsOpenfire pugins: Asterisk, Facebook i GmailCom a productes secundaris tenim els clients necessaris per poder utilitzar l'appliance:Firefox: Navegador web que servirà com a interfície d'usuari per les diferents eines d'administració i la demostració.Pigdin o Spark: Clients de missatgeria instantània, per l'appliance Comunicacions Unificades.A més d'instal·lar aquests productes, s'implementa una interfície web, mitjançant Drupal, en format HTML per enllaçar les diferents eines d'administració dels productes, per a cadascun dels dos appliances i es realitzara un Kiosk appliance per a familiaritzar-se amb l'entorn SuseStudio.

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Conformations of poly{G}-poly{C} π stacks with high hole mobility

Charge transfer properties of DNA depend strongly on the π stack conformation. In the present paper, we identify conformations of homogeneous poly-{G}-poly-{C} stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V2, between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G15. The average value of the coupling squared 〈 V2 〉 is found to be 0.0065 eV2. Then we analyze the base-pair and step parameters of the configurations in which V2 is at least an order of magnitude larger than 〈 V2 〉. To obtain more consistent data, ∼65 000 configurations of the (G:C)2 stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures (twist<20°) are of special interest, because the π stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist=30° and 35°, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation (twist38°) seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics

Binding energy and momentum distribution of nuclear matter using Green's functions methods

The influence of hole-hole (h-h) propagation in addition to the conventional particle-particle (p-p) propagation, on the energy per particle and the momentum distribution is investigated for the v2 central interaction which is derived from Reid¿s soft-core potential. The results are compared to Brueckner-Hartree-Fock calculations with a continuous choice for the single-particle (SP) spectrum. Calculation of the energy from a self-consistently determined SP spectrum leads to a lower saturation density. This result is not corroborated by calculating the energy from the hole spectral function, which is, however, not self-consistent. A generalization of previous calculations of the momentum distribution, based on a Goldstone diagram expansion, is introduced that allows the inclusion of h-h contributions to all orders. From this result an alternative calculation of the kinetic energy is obtained. In addition, a direct calculation of the potential energy is presented which is obtained from a solution of the ladder equation containing p-p and h-h propagation to all orders. These results can be considered as the contributions of selected Goldstone diagrams (including p-p and h-h terms on the same footing) to the kinetic and potential energy in which the SP energy is given by the quasiparticle energy. The results for the summation of Goldstone diagrams leads to a different momentum distribution than the one obtained from integrating the hole spectral function which in general gives less depletion of the Fermi sea. Various arguments, based partly on the results that are obtained, are put forward that a self-consistent determination of the spectral functions including the p-p and h-h ladder contributions (using a realistic interaction) will shed light on the question of nuclear saturation at a nonrelativistic level that is consistent with the observed depletion of SP orbitals in finite nuclei.

Wave-height hazard analysis in Eastern Coast of Spain : Bayesian approach using generalized Pareto distribution

Standard practice of wave-height hazard analysis often pays little attention to the uncertainty of assessed return periods and occurrence probabilities. This fact favors the opinion that, when large events happen, the hazard assessment should change accordingly. However, uncertainty of the hazard estimates is normally able to hide the effect of those large events. This is illustrated using data from the Mediterranean coast of Spain, where the last years have been extremely disastrous. Thus, it is possible to compare the hazard assessment based on data previous to those years with the analysis including them. With our approach, no significant change is detected when the statistical uncertainty is taken into account. The hazard analysis is carried out with a standard model. Time-occurrence of events is assumed Poisson distributed. The wave-height of each event is modelled as a random variable which upper tail follows a Generalized Pareto Distribution (GPD). Moreover, wave-heights are assumed independent from event to event and also independent of their occurrence in time. A threshold for excesses is assessed empirically. The other three parameters (Poisson rate, shape and scale parameters of GPD) are jointly estimated using Bayes' theorem. Prior distribution accounts for physical features of ocean waves in the Mediterranean sea and experience with these phenomena. Posterior distribution of the parameters allows to obtain posterior distributions of other derived parameters like occurrence probabilities and return periods. Predictives are also available. Computations are carried out using the program BGPE v2.0

The seasonal evolution of high vertical–mode internal waves in a deep reservoir

The causal mechanism and seasonal evolution of the internal wave field in a deep, warm, monomictic reservoirare examined through the analysis of field observations and numerical techniques. The study period extends fromthe onset of thermal stratification in the spring until midsummer in 2005. During this time, wind forcing wasperiodic, with a period of 24 h (typical of land–sea breezes), and the thermal structure in the lake wascharacterized by the presence of a shallow surface layer overlying a thick metalimnion, typical of small to mediumsized reservoirs with deep outtakes. Basin-scale internal seiches of high vertical mode (ranging from mode V3 toV5) were observed in the metalimnion. The structure of the dominant modes of oscillation changed asstratification evolved on seasonal timescales, but in all cases, their periods were close to that of the local windforcing (i.e., 24 h), suggesting a resonant response. Nonresonant oscillatory modes of type V1 and V2 becamedominant after large frontal events, which disrupted the diurnal periodicity of the wind forcing