Imaging magnetic excitations in confined magnetic structures

In this paper we revisit some particular aspects concerning the dynamic magnetization of thin Ni80Fe20 discs. In particular we address details of the excitation spectrum of Ni80Fe20 discs subjected to in-plane magnetic cw microwave fields. In this case imaging the dynamic magnetization allows us to estimate the internal magnetic field of the ferromagnetic element

Magnetic Vortex Core Reversal by Excitation of Spin Waves

Micron-sized magnetic platelets in the flux closed vortex state are characterized by an in-plane curling magnetization and a nanometer-sized perpendicularly magnetized vortex core. Having the simplest non-trivial configuration, these objects are of general interest to micromagnetics and may offer new routes for spintronics applications. Essential progress in the understanding of nonlinear vortex dynamics was achieved when low-field core toggling by excitation of the gyrotropic eigenmode at sub-GHz frequencies was established. At frequencies more than an order of magnitude higher vortex state structures possess spin wave eigenmodes arising from the magneto-static interaction. Here we demonstrate experimentally that the unidirectional vortex core reversal process also occurs when such azimuthal modes are excited. These results are confirmed by micromagnetic simulations which clearly show the selection rules for this novel reversal mechanism. Our analysis reveals that for spin wave excitation the concept of a critical velocity as the switching condition has to be modified.Comment: Minor corrections and polishing of previous versio

Minkowski Tensors of Anisotropic Spatial Structure

This article describes the theoretical foundation of and explicit algorithms for a novel approach to morphology and anisotropy analysis of complex spatial structure using tensor-valued Minkowski functionals, the so-called Minkowski tensors. Minkowski tensors are generalisations of the well-known scalar Minkowski functionals and are explicitly sensitive to anisotropic aspects of morphology, relevant for example for elastic moduli or permeability of microstructured materials. Here we derive explicit linear-time algorithms to compute these tensorial measures for three-dimensional shapes. These apply to representations of any object that can be represented by a triangulation of its bounding surface; their application is illustrated for the polyhedral Voronoi cellular complexes of jammed sphere configurations, and for triangulations of a biopolymer fibre network obtained by confocal microscopy. The article further bridges the substantial notational and conceptual gap between the different but equivalent approaches to scalar or tensorial Minkowski functionals in mathematics and in physics, hence making the mathematical measure theoretic method more readily accessible for future application in the physical sciences

Tissue engineering for the diaphragm and its various therapeutic possibilities - a systematic review

Diaphragmatic impairments exhibit high morbidity as well as mortality while current treatment options remain unsatisfactory. Tissue engineering (TE) approaches have explored the generation of an optimal biocompatible scaffold for diaphragmatic repair through tissue decellularization or de novo construction, with or without the addition of cells. We conducted a systematic review on the current state of the art in diaphragmatic tissue engineering (DTE) and found 24 articles eligible for final synthesis. The included approaches studied decellularization-based graft generation (9) and de novo bioscaffold construction (9). Three studies focused on in vitro host-scaffold interaction with synthesized, recellularized grafts (2) and decellularized extracellular matrix scaffolds (1). Another three studies investigated evaluation tools for decellularization efficacy. Among all studies, recellularization was performed in both decellularization-based (4) and de novo generated scaffolds (4). De novo constructed biocomposites as well as decellularized and recellularized scaffolds induced pro-regenerative remodeling and recovery of diaphragmatic function in all examined animal models. Potential therapeutic applications comprise substance defects requiring patch repair, such as congenital diaphragmatic hernia, and functional diseases demanding an entire organ transplant, like muscular dystrophies or dysfunction after prolonged artificial respiration

Commensurability oscillations in the rf conductivity of unidirectional lateral superlattices: measurement of anisotropic conductivity by coplanar waveguide

We have measured the rf magnetoconductivity of unidirectional lateral superlattices (ULSLs) by detecting the attenuation of microwave through a coplanar waveguide placed on the surface. ULSL samples with the principal axis of the modulation perpendicular (S_perp) and parallel (S_||) to the microwave electric field are examined. For low microwave power, we observe expected anisotropic behavior of the commensurability oscillations (CO), with CO in samples S_perp and S_|| dominated by the diffusion and the collisional contributions, respectively. Amplitude modulation of the Shubnikov-de Haas oscillations is observed to be more prominent in sample S_||. The difference between the two samples is washed out with the increase of the microwave power, letting the diffusion contribution govern the CO in both samples. The failure of the intended directional selectivity in the conductivity measured with high microwave power is interpreted in terms of large-angle electron-phonon scattering.Comment: 8 pages, 5 figure

Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories

Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation

The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6522 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P212121, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation.This research was funded by the Spanish Ministry of Science and Innovation and Ministry of Economy and Competitiveness and FEDER (EU): BIO2009-13261-C02-01/02 (ACA); BIO2012-39922-C02-01/02 (ACA); CTQ2013-4493 (JLN) and CSD2008-00005 (JLN); Andalusian Regional Government (Spain) and FEDER (EU): P09-CVI-5063 (ACA); and Valentian Regional Government (Spain) and FEDER (EU): Prometeo 2013/018 (JLN). Data collection was supported by European Synchrotron Radiation Facility (ESRF), Grenoble, France: BAG proposals MX-1406 (ACA) and MX-1541 (ACA); and ALBA (Barcelona, Spain) proposals 2012010072 (ACA) and 2012100378 (ACA)

Evaluation of the Allergenicity Potential of TcPR-10 Protein from Theobroma cacao

Background: The pathogenesis related protein PR10 (TcPR-10), obtained from the Theobroma cacao-Moniliophthora perniciosa interaction library, presents antifungal activity against M. perniciosa and acts in vitro as a ribonuclease. However, despite its biotechnological potential, the TcPR-10 has the P-loop motif similar to those of some allergenic proteins such as Bet v 1 (Betula verrucosa) and Pru av 1 (Prunus avium). The insertion of mutations in this motif can produce proteins with reduced allergenic power. The objective of the present work was to evaluate the allergenic potential of the wild type and mutant recombinant TcPR-10 using bioinformatics tools and immunological assays. Methodology/Principal Findings: Mutant substitutions (T10P, I30V, H45S) were inserted in the TcPR-10 gene by sitedirected mutagenesis, cloned into pET28a and expressed in Escherichia coli BL21(DE3) cells. Changes in molecular surface caused by the mutant substitutions was evaluated by comparative protein modeling using the three-dimensional structure of the major cherry allergen, Pru av 1 as a template. The immunological assays were carried out in 8-12 week old female BALB/c mice. The mice were sensitized with the proteins (wild type and mutants) via subcutaneous and challenged intranasal for induction of allergic airway inflammation. Conclusions/Significance: We showed that the wild TcPR-10 protein has allergenic potential, whereas the insertion of mutations produced proteins with reduced capacity of IgE production and cellular infiltration in the lungs. On the other hand, in vitro assays show that the TcPR-10 mutants still present antifungal and ribonuclease activity against M. perniciosa RNA. In conclusion, the mutant proteins present less allergenic potential than the wild TcPR-10, without the loss of interesting biotechnological properties. (Résumé d'auteur