Structural studies on FF domains by NMR spectroscopy

Descripció del recurs: el 26 de març de 2010El present treball s'ha realitzat en el marc del Programa de Biologia Estructural i Computacional de l'IRB Barcelona, en el grup de RMN de proteïnes, sota la direcció de la Dra María J. Macías. L'interès del grup d'investigació se centra en la determinació estructural de dominis de proteïna, en l'estudi d'interaccions i en entendre els mecanismes per a la seva regulació. Concretament, aquest treball està enfocat en l'estudi estructural de dominis FF. En el nostre grup es va començar a estudiar els dominis FF a partir de l'observació que aquests dominis es troben sovint en proteïnes que també contenen WW, un petit domini d'interacció proteïna-proteïna que ha estat i continua sent la línia d'investigació principal del grup, i del qual s'han realitzat nombrosos i detallats estudis. En canvi, el dominis FF han estat identificats fa poc temps i la informació estructural i funcional de la qual es disposa és, a dia d'avui, escassa. En part, el pocs estudis realitzats amb aquests dominis pot ser conseqüència de que només els trobem en un conjunt reduït de proteïnes. De fet, la seva presència es limita a tres famílies de proteïnes: els factors d'splicing FBP11, Prp40 i URN1, el factor de transcripció CA150 i una família de proteïnes reguladores de RhoGTPases, les p190 RhoGAPs. Al meu grup, l'estudi amb dominis FF es va iniciar amb la resolució de l'estructura tridimensional del primer FF de la proteïna Prp40 de llevat, que va representar la segona estructura resolta per a un domini FF. En aquest treball l'objectiu ha estat aprofundir en el coneixement dels dominis FF, bàsicament des d'un punt de vista estructural utilitzant com a tècnica principal la resonànica magnètica nuclear (RMN). Aquesta tesi doctoral s'ha dividit en tres parts i en cada una d'elles s'ha treballat amb els dominis FF de les tres famílies de proteïnes esmentades anteriorment. L'enfoc també ha estat lleugerament diferent a cada part. Així, en el primer capítol, centrat en els dominis FF presents als factors d'splicing URN1 i Prp40, el gruix de la feina va ser l'obtenció de noves estructures tridimensionals per RMN d'aquests dominis. En canvi, en el segon capítol ens vam centrar en l'estudi de la interacció dels dominis FF de CA150 amb el seu primer lligand descrit, un motiu doble fosforilat del domini C-terminal de la RNA-polimerasa II (fosfo-CTD). Finalment, en la tercera part l'interès es va dirigir a l'estudi de la regulació de l'associació dels dominis FF de p190-A RhoGAP amb el factor de transcripció TFII-I, per mitjà d'una fosforilació sobre el primer FF de p190-A RhoGAP.The present work has been done in the protein NMR group from the Structural and Computational Biology at the IRB Barcelona, under the direction of Dr. Maria J. Macias. The group's main interest is the structural determination of protein domains, in the study of their interactions and in the understanding of the mechanisms for their regulation. In particular, this work is focused in the structural study of FF domains. In our group, the study of FF domains began from the observation that these domains are often found in proteins that also contain WW domains, a small protein-protein interaction domain that has been, and continues to be the central research line of the group and that has been object of numerous and detailed studies. Conversely, FF domains have been recently identified and the structural and functional information available on them is, to date, limited. One of the reasons of the few studies reported for these domains could be consequence of their reduced presence in proteins. In fact, FF domains are only present in three protein families: the splicing factors FBP11, Prp40 and URN1, the transcription factor CA150 and a family of RhoGTPase regulators, the p190 RhoGAPs. In our group, the work with FF domains started with the solution of the three-dimensional structure of the first FF domain from yeast Prp40, which just represented the second solved structure for an FF domain. In the present work the aim has been to gain insight into FF domain knowledge, basically from a structural point of view, using nuclear magnetic resonance (NMR) as the principal methodology for the structural studies

Key Figures on the Alt Empordà 2020

Demografia; Salut; Economia; TerritoriDemografía; Salud; Economía; TerritorioDemographics; Health; Economy; TerritoryL’objectiu d’aquest document és proporcionar un conjunt de visualitzacions intuïtives, clares i concises sobre alguns dels indicadors disponibles de l’Alt Empordà amb la intenció d’aportar una mirada estratègica de l’estat actual de la comarca.El objetivo de este documento es proporcionar un conjunto de visualizaciones intuitivas, claras y concisas sobre algunos de los indicadores disponibles del Alt Empordà con la intención de aportar una visión estratégica del estado actual de la comarca.The objective of this document is to provide a series of intuitive, clear and concise visualisations of some of the available figures on the Alt Empordà to provide a strategic view of the current state of the region

Key Figures on the Alt Empordà 2021

Demografia; Salut; Economia; TerritoriDemografía; Salud; Economía; TerritorioDemographics; Health; Economy; TerritoryIndicadores Clave del Alt Empordà 2021 presenta una selección de datos estadísticos sobre el Alt Empordà y la demarcación de Girona. Estos datos se enmarcan en el ámbito municipal en todos aquellos casos en que ha sido posible pero en muchos otros no se ha podido obtener información detallada, por lo que las cifras son de ámbito comarcal o provincial. Este documento quiere aportar una visión general que facilite conocer el estado del territorio en el momento de la publicación: las tendencias recientes, incluyendo datos demográficos, sociodemográficos, de salud, economía, territorio y sus recursos.Key Figures on the Alt Empordà 2021 presents a selection of statistics on the Alt Empordà and the area of Girona. Whenever possible, these data are defined within the municipal scope, but in many cases it has not been possible to obtain sufficiently detailed information, so the figures are regional or provincial. This document aims to provide a general view to help know the state of the area at the time of publication: recent trends, including data on demographics, socio-demographics, health, economy, the territory and its resources

Key Figures on Alt Empordà 2022

Demografia; Salut; Economia; TerritoriDemografía; Salud; Economía; TerritorioDemographics; Health; Economy; TerritoryIndicadors Clau de l’Alt Empordà 2022 presenta una selecció de dades estadístiques sobre l’Alt Empordà i la demarcació de Girona. Aquestes dades s’emmarquen en l’àmbit municipal en tots aquells casos en què ha estat possible i, en altres en què no s’ha pogut obtenir informació prou detallada, es presenten en àmbit comarcal o provincial. En aquest document es vol aportar una visió general que faciliti conèixer l’estat del territori amb dades de l’any 2021 o les més recents editades, i veure quines són les tendències actuals. El recull inclou dades sociodemogràfiques, de salut, d’economia, de medi ambient i d’altres recursos del territori. En l’edició de 2022, com ja passava l’any anterior, s’objectiva la influència de l'epidèmia de COVID-19 en diversos indicadors i tendències.Indicadores Clave del Alt Empordà 2022 presenta una selección de datos estadísticos sobre el Alt Empordà y la demarcación de Girona. Estos datos se enmarcan en el ámbito municipal en todos aquellos casos en los que ha sido posible y, en los que no se ha podido obtener información lo suficientemente detallada, se presentan en ámbito comarcal o provincial. En este documento se quiere aportar una visión general que facilite conocer el estado del territorio con datos del año 2021 o más recientes editados, y ver cuáles son las tendencias actuales. La recopilación incluye datos sociodemográficos, de salud, de economía, de medio ambiente y otros recursos del territorio. En la edición de 2022, como ya pasaba el año anterior, se objetiva la influencia de la epidemia de COVID-19 en varios indicadores y tendencias.Key Figures on Alt Empordà 2022 presents a selection of statistics on Alt Empordà and the province of Girona. Whenever possible, this data is defined within the municipal scope, but in many cases, it has not been possible to obtain sufficiently detailed information, so the figures are for the whole area or provincial. This document aims to provide a general view to help us find out about the state of the area using 2021 data or the most recent data available and identifying current trends. This document includes data on demographics, socio-demographics, health, economy, the territory and its resources. As was the case last year, in the 2022 edition, the influence of the COVID-19 epidemic has been objectified in various indicators and trends

Comparison of two-drug combinations, amikacin/tigecycline/imipenem and amikacin/tigecycline/clarithromycin against Mycobacteroides abscessus subsp. abscessus using the in vitro time-kill assay

Nontuberculous mycobacteria include 198 mycobacterial species. Among these, Mycobacteroides abscessus is a rapidly growing mycobacteria that causes lung and skin infections. M. abscessus lung infections are difficult to treat due to the high levels of resistance to several classes of antibiotics. The current treatment is based on combining at least two or three antibiotics. However, treatment outcomes remain very poor. The objective was to compare the in vitro activity of amikacin, tigecycline, imipenem, and clarithromycin, alone and in two different three-drug combinations (amikacin/tigecycline/imipenem and amikacin/tigecycline/clarithromycin) against seven M. abscessus subsp. abscessus clinical isolates using the time-kill assay. The two combinations showed greater activity than the antibiotics tested individually. Even though both combinations showed similar activity as well as no antagonistic activity, the combination including imipenem could not be an alternative treatment against M. abscessus subsp. abscessus lung infections caused by clarithromycin susceptible isolates. However, this combination could be considered against clarithromycin resistant isolates. Future studies are necessary to confirm this hypothesis

A curvilinear high order finite element framework for electromechanics: From linearised electro-elasticity to massively deformable dielectric elastomers

This paper presents a high order finite element implementation of the convex multi-variable electro-elasticity for large deformations large electric fields analyses and its particularisation to the case of small strains through a staggered scheme. With an emphasis on accurate geometrical representation, a high performance curvilinear finite element framework based on an a posteriori mesh deformation technique is developed to accurately discretise the underlying displacement-potential variational formulation. The performance of the method under near incompressibility and bending actuation scenarios is analysed with extremely thin and highly stretched components and compared to the performance of mixed variational principles recently reported by Gil and Ortigosa [1, 2, 3]. Although convex multi-variable constitutive models are elliptic hence, materially stable for the entire range of deformations and electric fields, other forms of physical instabilities are not precluded in these models. In particular, physical instabilities present in dielectric elastomers such as pull-in instability, snap-through and the formation, propagation and nucleation of wrinkles and folds are numerically studied with a detailed precision in this paper, verifying experimental findings. For the case of small strains, the essence of the approach taken lies in guaranteeing the objectivity of the resulting work conjugates, by starting from the underlying convex multi-variable internal energy, whence avoiding the need for further symmetrisation of the resulting Maxwell and Minkowski-type stresses at small strain regime. In this context, the nonlinearity with respect to electrostatic counterparts such as electric displacements is still retained, hence resulting in a formulation similar but more competitive with the existing linearised electro-elasticity approaches. Virtual prototyping of many application-oriented dielectric elastomers are carried out with an eye on pattern forming in soft robotics and other potential medical applications

A unified approach for a posteriori high-order curved mesh generation using solid mechanics

The paper presents a unified approach for the a posteriori generation of arbitrary high-order curvilinear meshes via a solid mechanics analogy. The approach encompasses a variety of methodologies, ranging from the popular incremental linear elastic approach to very sophisticated non-linear elasticity. In addition, an intermediate consistent incrementally linearised approach is also presented and applied for the first time in this context. Utilising a consistent derivation from energy principles, a theoretical comparison of the various approaches is presented which enables a detailed discussion regarding the material characterisation (calibration) employed for the different solid mechanics formulations. Five independent quality measures are proposed and their relations with existing quality indicators, used in the context of a posteriori mesh generation, are discussed. Finally, a comprehensive range of numerical examples, both in two and three dimensions, including challenging geometries of interest to the solids, fluids and electromagnetics communities, are shown in order to illustrate and thoroughly compare the performance of the different methodologies. This comparison considers the influence of material parameters and number of load increments on the quality of the generated high-order mesh, overall computational cost and, crucially, the approximation properties of the resulting mesh when considering an isoparametric finite element formulation

On a family of numerical models for couple stress based flexoelectricity for continua and beams

A family of numerical models for the phenomenological linear flexoelectric theory for continua and their particularisation to the case of three-dimensional beams based on a skew-symmetric couple stress theory is presented. In contrast to the standard strain gradient flexoelectric models which assume coupling between electric polarisation and strain gradients, we postulate an electric enthalpy in terms of linear invariants of curvature and electric field. This is achieved by introducing the axial (mean) curvature vector as a strain gradient measure. The physical implication of this assumption is many-fold. Firstly, analogous to the standard strain gradient models, for isotropic (non-piezoelectric) materials it allows constructing flexoelectric energies without breaking material’s centrosymmetry. Secondly, unlike the standard strain gradient models, nonuniform distribution of volumetric part of strains (volumetric strain gradients) do not generate electric polarisation, as also confirmed by experimental evidence to be the case for some important classes of flexoelectric materials. Thirdly, a state of plane strain generates out of plane deformation through strain gradient effects. Finally, under this theory, extension and shear coupling modes cannot be characterised individually as they contribute to the generation of electric polarisation as a whole. As a first step, a detailed comparison of the developed couple stress based flexoelectric model with the standard strain gradient flexoelectric models is performed for the case of Barium Titanate where a myriad of simple analytical solutions are assumed in order to quantitatively describe the similarities and dissimilarities in effective electromechanical coupling under these two theories. From a physical point of view, the most notable insight gained is that, if the same experimental flexoelectric constants are fitted in to both theories, the presented theory in general, reports up to 200% stronger electromechanical conversion efficiency. From the formulation point of a view, the presented flexoelectric model is also competitively simpler as it eliminates the need for high order strain gradient and coupling tensors and can be characterised by a single flexoelectric coefficient. In addition, three distinct mixed flexoelectric variational principles are presented for both continuum and beam models that facilitate incorporation of strain gradient measures in to a standard finite element scheme while maintaining the C0 continuity. Consequently, a series of low and high order mixed finite element schemes for couple stress based flexoelectricity are presented and thoroughly benchmarked against available closed form solutions in regards to electromechanical coupling efficiency. Finally, nanocompression of a complex flexoelectric conical pyramid for which analytical solution cannot be established is numerically studied where curvature induced necking of the specimen and vorticity around the frustum generate moderate electric polarisation

Inhibition of Sema-3A Promotes Cell Migration, Axonal Growth, and Retinal Ganglion Cell Survival

Semaphorin 3A (Sema-3A) is a secreted protein that deflects axons from inappropriate regions and induces neuronal cell death. Intravitreal application of polyclonal antibodies against Sema-3A prevents loss of retinal ganglion cells ensuing from axotomy of optic nerves. This suggested a therapeutic approach for neuroprotection via inhibition of the Sema-3A pathway.Funded by the EU seventh framework program, Grant Agreement #604884.Peer reviewe

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15–18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution