Functional Characterisation of Alpha-Galactosidase A Mutations as a Basis for a New Classification System in Fabry Disease

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The study has been supported partially by an unrestricted scientific grant from Shire Human Genetic Therapies (Germany

Electrical conduction of silicon oxide containing silicon quantum dots

Current-voltage measurements have been made at room temperature on a Si-rich silicon oxide film deposited via Electron-Cyclotron Resonance Plasma Enhanced Chemical Vapor Deposition (ECR-PECVD) and annealed at 750 - 1000$^\circ$C. The thickness of oxide between Si quantum dots embedded in the film increases with the increase of annealing temperature. This leads to the decrease of current density as the annealing temperature is increased. Assuming the Fowler-Nordheim tunneling mechanism in large electric fields, we obtain an effective barrier height $\phi_{eff}$ of $\sim$ 0.7 $\pm$ 0.1 eV for an electron tunnelling through an oxide layer between Si quantum dots. The Frenkel-Poole effect can also be used to adequately explain the electrical conduction of the film under the influence of large electric fields. We suggest that at room temperature Si quantum dots can be regarded as traps that capture and emit electrons by means of tunneling.Comment: 14 pages, 5 figures, submitted to J. Phys. Conden. Mat

Pembuatan Peta Zona Nilai Ekonomi Kawasan (Znek) Menggunakan Tcm (Travel Cost Method) Dan Cvm (Contingent Valuation Method) Berbasis Sistem Informasi Geografis (Studi Kasus : Candi Prambanan)

Prambanan Temple has potential as a tourist attraction. The strategic location which have historical value, makes this Place became one tourist destination areas Klaten. Based on this, we need a Zone Map Economic Value Areas (ZNEK) to the Prambanan area of the palace to estimate the economic value and benefits based on willingness to pay (WTP) tourists and the people who benefit from the region. Sampling method (respondents) were used in this research is non probability sampling with accidental sampling technique, where respondents are those who by chance / accidental encountered in the study area and can be used as a sample, if it is considered that the person who happened to be found suitable as a data source. Data processing method used is multiple linear regression analysis and calculation software WTP using Maple 17.Results obtained from the study of this final project is the Economic Value Area Zone maps with the total value of economic attraction Prambanan Temple Rp.32.851.020.029.000,- Maps generated from the integration of economic and spatial aspects can be used as an objective consideration of the decision-making process in the spatial field and economic field for the government to optimize and simplify the process of the asset\u27s management and monitoring the natural resources potential. Besides being able to provide a solution for the management of resource constraints of the economy in various regions in Indonesia, the map can be used too as a learning tool for the public society to bring awareness of the importance of potential belonging

Inducible fluorescent speckle microscopy

The understanding of cytoskeleton dynamics has benefited from the capacity to generate fluorescent fiducial marks on cytoskeleton components. Here we show that light-induced imprinting of three-dimensional (3D) fluorescent speckles significantly improves speckle signal and contrast relative to classic (random) fluorescent speckle microscopy. We predict theoretically that speckle imprinting using photobleaching is optimal when the laser energy and fluorophore responsivity are related by the golden ratio. This relation, which we confirm experimentally, translates into a 40% remaining signal after speckle imprinting and provides a rule of thumb in selecting the laser power required to optimally prepare the sample for imaging. This inducible speckle imaging (ISI) technique allows 3D speckle microscopy to be performed in readily available libraries of cell lines or primary tissues expressing fluorescent proteins and does not preclude conventional imaging before speckle imaging. As a proof of concept, we use ISI to measure metaphase spindle microtubule poleward flux in primary cells and explore a scaling relation connecting microtubule flux to metaphase duration.H. Maiato is funded by the seventh framework program grant PRE CISE from the European Research Council, FLAD Life Science 2020, and the Louis-Jeantet Young Investigator Career Award

Size-Dependent Indirect Excitation of Trivalent Er Ions via Si Nanocrystals Embedded in a Silicon-Rich Silicon Oxide Matrix Deposited by ECR-PECVD

Silicon nanocrystals (Si-nc) embedded in a silicon-rich silicon oxide matrix codoped with Er3+ ions have been fabricated by electron-cyclotron plasma-enhanced chemical vapor deposition. Indirect excitation of erbium photoluminescence via silicon nanocrystals has been obtained within a broad pump wavelength range. The influence of different nanocrystal sizes on the excitation transfer from the Si-nc to Er3+ ions is discussed

Identification of direct residue contacts in protein-protein interaction by message passing

Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes enables various statistical approaches to this problem. In this context covariance-based methods have been used to identify correlation between amino acid positions in interacting proteins. However, these methods have an important shortcoming, in that they cannot distinguish between directly and indirectly correlated residues. We developed a method that combines covariance analysis with global inference analysis, adopted from use in statistical physics. Applied to a set of >2,500 representatives of the bacterial two-component signal transduction system, the combination of covariance with global inference successfully and robustly identified residue pairs that are proximal in space without resorting to ad hoc tuning parameters, both for heterointeractions between sensor kinase (SK) and response regulator (RR) proteins and for homointeractions between RR proteins. The spectacular success of this approach illustrates the effectiveness of the global inference approach in identifying direct interaction based on sequence information alone. We expect this method to be applicable soon to interaction surfaces between proteins present in only 1 copy per genome as the number of sequenced genomes continues to expand. Use of this method could significantly increase the potential targets for therapeutic intervention, shed light on the mechanism of protein-protein interaction, and establish the foundation for the accurate prediction of interacting protein partners.Comment: Supplementary information available on http://www.pnas.org/content/106/1/67.abstrac

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.This work was financially supported by the following grants: project GABI-BARLEX, German Federal Ministry of Education and Research (BMBF), #0314000 to MP, US, KFXM and NS; Triticeae Coordinated Agricultural Project, USDA-NIFA #2011-68002-30029 to GJM; and Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA’s Cooperative State Research and Extension Service, #2009-65300- 05645 to GJM

Luminescence properties of Ce3+ and Tb3+ co-doped SiOxNy thin films: Prospects for color tunability in silicon-based hosts

In this work, the role of the nitrogen content, the annealing temperature, and the sample morphology on the luminescence properties of Ce3+ and Tb3+ co-doped SiOxNy thin films has been investigated. An increasing nitrogen atomic percentage has been incorporated in the host matrix by gradually replacing oxygen with nitrogen during fabrication while maintaining the Si content unaltered, obtaining a sequential variation in the film composition from nearly stoichiometric SiO2 to SiOxNy. The study of rare earth doped single layers has allowed us to identify the parameters that yield an optimum optical performance from Ce3+ and Tb3+ ions. Ce3+ ions proved to be highly sensitive to the annealing temperature and the nitrogen content, showing strong PL emission for relatively low nitrogen contents (from 0 to 20%) and moderate annealing temperatures (800-1000 degrees C) or under high temperature annealing (1180 degrees C). Tb3+ ions, on the other hand, displayed a mild dependence on those film parameters. Rare earth co-doping has also been investigated by comparing the luminescence properties of three different approaches: (i) a Ce3+ and Tb3+ co-doped SiOxNy single layer, (ii) a bilayer composed of two SiOxNy single layers doped with either Ce3+ or Tb3+ ions, and (iii) a multilayer composed of a series of either Tb3+ or Ce3+-doped SiOxNy thin films with interleaved SiO2 spacers. Bright green emission and efficient energy transfer from either Ce3+ ions or Ce silicates to Tb3+ ions has been observed in the co-doped single layer as a consequence of the strong ion-ion interaction. On the other hand, independent luminescence from Ce3+ and Tb3+ ions has been observed in the Ce3+ and Tb3+ co-doped bilayer and multilayer, providing a good scenario to develop light emitting devices with wide color tunability by varying the number of deposited films that contain each rare earth dopant. Moreover, the optoelectronic properties of Ce3+-and/or Tb3+-doped thin films have been studied by depositing transparent conductive electrodes over selected samples. An electroluminescence signal according to the rare earth transitions is obtained in all cases, validating the excitation of Ce3+ and Tb3+ ions upon electron injection. Also, the main charge transport of injected electrons has been evaluated and correlated with the layer stoichiometry. Finally, a simple reliability test has allowed disclosing the origin of the early breakdown of test devices, attributed to the excessive joule heating at filament currents that occur around a region close to the polarization point. (C) 2016 AIP Publishing LLC.This research was supported by the Spanish Ministry of Science and Innovation (TEC2012-38540-C02-01). RBS characterization was performed in the Tandetron Accelerator Laboratory at Western University in London, ON (Canada). TEM characterization was carried out in the Science and Technical Centers (CCiT) of the University of Barcelona. In Canada, this work was supported by the Natural Sciences and Engineering Research Council (NSERC) under the Discovery Grants program.Ramirez, JM.; Ruiz-Caridad, A.; Wojcik, J.; Gutiérrez Campo, AM.; Estrade, S.; Peiro, F.; Sanchis Kilders, P.... (2016). Luminescence properties of Ce3+ and Tb3+ co-doped SiOxNy thin films: Prospects for color tunability in silicon-based hosts. Journal of Applied Physics. 119(11):113108-1-113108-14. https://doi.org/10.1063/1.4944433S113108-1113108-141191

A Genome Assembly of the Barley 'Transformation Reference' Cultivar Golden Promise

Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv. Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv. Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments

Relationships between Root Pathogen Resistance, Abundance and Expression of Pseudomonas Antimicrobial Genes, and Soil Properties in Representative Swiss Agricultural Soils

Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant diseases have often been isolated from soils defined as disease-suppressive, i.e., soils, in which specific plant pathogens are present, but plants show no or reduced disease symptoms. Moreover, it is assumed that pseudomonads producing antimicrobial compounds such as 2,4-diacetylphloroglucinol (DAPG) or phenazines (PHZ) contribute to the specific disease resistance of suppressive soils. However, pseudomonads producing antimicrobial metabolites are also present in soils that are conducive to disease. Currently, it is still unknown whether and to which extent the abundance of antimicrobials-producing pseudomonads is related to the general disease resistance of common agricultural soils. Moreover, virtually nothing is known about the conditions under which pseudomonads express antimicrobial genes in agricultural field soils. We present here results of the first side-by-side comparison of 10 representative Swiss agricultural soils with a cereal-oriented cropping history for (i) the resistance against two soilborne pathogens, (ii) the abundance of Pseudomonas bacteria harboring genes involved in the biosynthesis of the antimicrobials DAPG, PHZ, and pyrrolnitrin on roots of wheat, and (iii) the ability to support the expression of these genes on the roots. Our study revealed that the level of soil disease resistance strongly depends on the type of pathogen, e.g., soils that are highly resistant to Gaeumannomyces tritici often are highly susceptible to Pythium ultimum and vice versa. There was no significant correlation between the disease resistance of the soils, the abundance of Pseudomonas bacteria carrying DAPG, PHZ, and pyrrolnitrin biosynthetic genes, and the ability of the soils to support the expression of the antimicrobial genes. Correlation analyses indicated that certain soil factors such as silt, clay, and some macro- and micronutrients influence both the abundance and the expression of the antimicrobial genes. Taken together, the results of this study suggests that pseudomonads producing DAPG, PHZ, or pyrrolnitrin are present and abundant in Swiss agricultural soils and that the soils support the expression of the respective biosynthetic genes in these bacteria to various degrees. The precise role that these pseudomonads play in the general disease resistance of the investigated agricultural soils remains elusive