Characterization of ion-beam-sputtered AlF3_3 thin films for gravitational-wave interferometers

Thermal noise in amorphous coatings is a limitation for a wide range of precision experiments such as gravitational-wave detectors (GWDs). Mirrors for GWDs are composed of multiple thin layers of dielectric materials deposited on a substrate: the stack is made of layers with a high refractive index interleaved with layers of a low refractive index. The goal is to obtain high reflectivity and low thermal noise. In this paper we report on the optical and mechanical properties of ion-beamsputtered aluminium fluoride (AlF3) thin films which have one of the lowest refractive index among the known coating materials and we discuss their application in current and future GWDs

Molecular Characterization of a Fus3/Kss1 Type MAPK from Puccinia striiformis f. sp. tritici, PsMAPK1

Puccinia striiformis f. sp. tritici (Pst) is an obligate biotrophic fungus that causes the destructive wheat stripe rust disease worldwide. Due to the lack of reliable transformation and gene disruption method, knowledge about the function of Pst genes involved in pathogenesis is limited. Mitogen-activated protein kinase (MAPK) genes have been shown in a number of plant pathogenic fungi to play critical roles in regulating various infection processes. In the present study, we identified and characterized the first MAPK gene PsMAPK1 in Pst. Phylogenetic analysis indicated that PsMAPK1 is a YERK1 MAP kinase belonging to the Fus3/Kss1 class. Single nucleotide polymerphisms (SNPs) and insertion/deletion were detected in the coding region of PsMAPK1 among six Pst isolates. Real-time RT-PCR analyses revealed that PsMAPK1 expression was induced at early infection stages and peaked during haustorium formation. When expressed in Fusarium graminearum, PsMAPK1 partially rescued the map1 mutant in vegetative growth and pathogenicity. It also partially complemented the defects of the Magnaporthe oryzae pmk1 mutant in appressorium formation and plant infection. These results suggest that F. graminearum and M. oryzae can be used as surrogate systems for functional analysis of well-conserved Pst genes and PsMAPK1 may play a role in the regulation of plant penetration and infectious growth in Pst

All life 2

The files contain the gene expression results from microarray experiments and matching elaborations reported in the paper entitled “Ataxia Teleangiectasia transcriptomic profile: low dose for long-time dexamethasone administration impacts”. Microarray analysis. Total RNA was extracted from all the used cell lines using the RNeasy kit plus (QIAGEN). Quality control of RNA was assayed by Nanodrop and by Agilent Bioanalyzer-TapeStation. Labelling procedure was performed by using Affymetrix GeneChip WT Pico kit as recommended by the manufacturer. The employed array chips were the Human Clariom D from Affymetrix and procedures were carried out as indicated by the manufacturer. The GeneChip Scanner 3000 7G platform was used for data acquisition. The data analysis, after pre-processing at probe level (CEL files), was performed by RMA background adjustment, quantile method for normalization and median polish for summarization. For the functional annotation of DEGs (differentially expressed genes) were selected by the Affymetrix TAC console, using an FDR p-value ≤0.05. Quantitative PCR Some of the genes resulting as modulated by dex were further investigated by qPCR. For this purpose, five hundred nanograms of RNA were employed in each experiment to obtain cDNA by PrimeScript™ RT Master Mix (Takara). One nanogram of cDNA was employed in each TaqMan Gene Expression Assay (Thermo Fisher Scientific) for the genes: FKBP5, HDAC4 and DDIT4, according to the manufacturer’s instructions. PPIC and PPIA gene expressions were used as housekeeping genes. Amplification plots were analysed using the ABI PRISM 7500 sequence detection system (Applied Biosystems) and the relative expression data were calculated by the ½ Ct method. Data analysis and functional networks Statistical analyses and graphs plotting were performed by GraphPad Prism. Statistical tests were chosen according to the sample size and variance homogeneity. The gene symbol lists resulting from the gene selection procedure and the matching gene expression values, were used to compute functional networks by using the Reactome (FI) Functional Interaction Network plugin for Cytoscape [34]. Biological processes (BP) and pathway enrichment of moduli were assessed by FDR p-value ≤0.01, while the whole network functions were computed by using FDR ≤0.1

All life 2

The files contain the gene expression results from microarray experiments and matching elaborations reported in the paper entitled “Ataxia Teleangiectasia transcriptomic profile: low dose for long-time dexamethasone administration impacts”. Microarray analysis. Total RNA was extracted from all the used cell lines using the RNeasy kit plus (QIAGEN). Quality control of RNA was assayed by Nanodrop and by Agilent Bioanalyzer-TapeStation. Labelling procedure was performed by using Affymetrix GeneChip WT Pico kit as recommended by the manufacturer. The employed array chips were the Human Clariom D from Affymetrix and procedures were carried out as indicated by the manufacturer. The GeneChip Scanner 3000 7G platform was used for data acquisition. The data analysis, after pre-processing at probe level (CEL files), was performed by RMA background adjustment, quantile method for normalization and median polish for summarization. For the functional annotation of DEGs (differentially expressed genes) were selected by the Affymetrix TAC console, using an FDR p-value ≤0.05. Quantitative PCR Some of the genes resulting as modulated by dex were further investigated by qPCR. For this purpose, five hundred nanograms of RNA were employed in each experiment to obtain cDNA by PrimeScript™ RT Master Mix (Takara). One nanogram of cDNA was employed in each TaqMan Gene Expression Assay (Thermo Fisher Scientific) for the genes: FKBP5, HDAC4 and DDIT4, according to the manufacturer’s instructions. PPIC and PPIA gene expressions were used as housekeeping genes. Amplification plots were analysed using the ABI PRISM 7500 sequence detection system (Applied Biosystems) and the relative expression data were calculated by DCt method and represented as 1/2^DCt. Data analysis and functional networks Statistical analyses and graphs plotting were performed by GraphPad Prism. Statistical tests were chosen according to the sample size and variance homogeneity. The gene symbol lists resulting from the gene selection procedure and the matching gene expression values, were used to compute functional networks by using the Reactome (FI) Functional Interaction Network plugin for Cytoscape [34]. Biological processes (BP) and pathway enrichment of moduli were assessed by FDR p-value ≤0.01, while the whole network functions were computed by using FDR ≤0.1

All life 2

The files contain the gene expression results from microarray experiments and matching elaborations reported in the paper entitled “Ataxia Teleangiectasia transcriptomic profile: low dose for long-time dexamethasone administration impacts”. Microarray analysis. Total RNA was extracted from all the used cell lines using the RNeasy kit plus (QIAGEN). Quality control of RNA was assayed by Nanodrop and by Agilent Bioanalyzer-TapeStation. Labelling procedure was performed by using Affymetrix GeneChip WT Pico kit as recommended by the manufacturer. The employed array chips were the Human Clariom D from Affymetrix and procedures were carried out as indicated by the manufacturer. The GeneChip Scanner 3000 7G platform was used for data acquisition. The data analysis, after pre-processing at probe level (CEL files), was performed by RMA background adjustment, quantile method for normalization and median polish for summarization. For the functional annotation of DEGs (differentially expressed genes) were selected by the Affymetrix TAC console, using an FDR p-value ≤0.05. Quantitative PCR Some of the genes resulting as modulated by dex were further investigated by qPCR. For this purpose, five hundred nanograms of RNA were employed in each experiment to obtain cDNA by PrimeScript™ RT Master Mix (Takara). One nanogram of cDNA was employed in each TaqMan Gene Expression Assay (Thermo Fisher Scientific) for the genes: FKBP5, HDAC4 and DDIT4, according to the manufacturer’s instructions. PPIC and PPIA gene expressions were used as housekeeping genes. Amplification plots were analysed using the ABI PRISM 7500 sequence detection system (Applied Biosystems) and the relative expression data were calculated by the ½ Ct method. Data analysis and functional networks Statistical analyses and graphs plotting were performed by GraphPad Prism. Statistical tests were chosen according to the sample size and variance homogeneity. The gene symbol lists resulting from the gene selection procedure and the matching gene expression values, were used to compute functional networks by using the Reactome (FI) Functional Interaction Network plugin for Cytoscape [34]. Biological processes (BP) and pathway enrichment of moduli were assessed by FDR p-value ≤0.01, while the whole network functions were computed by using FDR ≤0.1

All life 2

The files contain the gene expression results from microarray experiments and matching elaborations reported in the paper entitled “Ataxia Teleangiectasia transcriptomic profile: low dose for long-time dexamethasone administration impacts”. Microarray analysis. Total RNA was extracted from all the used cell lines using the RNeasy kit plus (QIAGEN). Quality control of RNA was assayed by Nanodrop and by Agilent Bioanalyzer-TapeStation. Labelling procedure was performed by using Affymetrix GeneChip WT Pico kit as recommended by the manufacturer. The employed array chips were the Human Clariom D from Affymetrix and procedures were carried out as indicated by the manufacturer. The GeneChip Scanner 3000 7G platform was used for data acquisition. The data analysis, after pre-processing at probe level (CEL files), was performed by RMA background adjustment, quantile method for normalization and median polish for summarization. For the functional annotation of DEGs (differentially expressed genes) were selected by the Affymetrix TAC console, using an FDR p-value ≤0.05. Quantitative PCR Some of the genes resulting as modulated by dex were further investigated by qPCR. For this purpose, five hundred nanograms of RNA were employed in each experiment to obtain cDNA by PrimeScript™ RT Master Mix (Takara). One nanogram of cDNA was employed in each TaqMan Gene Expression Assay (Thermo Fisher Scientific) for the genes: FKBP5, HDAC4 and DDIT4, according to the manufacturer’s instructions. PPIC and PPIA gene expressions were used as housekeeping genes. Amplification plots were analysed using the ABI PRISM 7500 sequence detection system (Applied Biosystems) and the relative expression data were calculated by DCt method and represented as 1/2^DCt. Data analysis and functional networks Statistical analyses and graphs plotting were performed by GraphPad Prism. Statistical tests were chosen according to the sample size and variance homogeneity. The gene symbol lists resulting from the gene selection procedure and the matching gene expression values, were used to compute functional networks by using the Reactome (FI) Functional Interaction Network plugin for Cytoscape [34]. Biological processes (BP) and pathway enrichment of moduli were assessed by FDR p-value ≤0.01, while the whole network functions were computed by using FDR ≤0.1

All life

The data contain

All life 2

The files contain the gene expression results from microarray experiments and matching elaborations reported in the paper entitled “Ataxia Teleangiectasia transcriptomic profile: low dose for long-time dexamethasone administration impacts”. Microarray analysis. Total RNA was extracted from all the used cell lines using the RNeasy kit plus (QIAGEN). Quality control of RNA was assayed by Nanodrop and by Agilent Bioanalyzer-TapeStation. Labelling procedure was performed by using Affymetrix GeneChip WT Pico kit as recommended by the manufacturer. The employed array chips were the Human Clariom D from Affymetrix and procedures were carried out as indicated by the manufacturer. The GeneChip Scanner 3000 7G platform was used for data acquisition. The data analysis, after pre-processing at probe level (CEL files), was performed by RMA background adjustment, quantile method for normalization and median polish for summarization. For the functional annotation of DEGs (differentially expressed genes) were selected by the Affymetrix TAC console, using an FDR p-value ≤0.05. Quantitative PCR Some of the genes resulting as modulated by dex were further investigated by qPCR. For this purpose, five hundred nanograms of RNA were employed in each experiment to obtain cDNA by PrimeScript™ RT Master Mix (Takara). One nanogram of cDNA was employed in each TaqMan Gene Expression Assay (Thermo Fisher Scientific) for the genes: FKBP5, HDAC4 and DDIT4, according to the manufacturer’s instructions. PPIC and PPIA gene expressions were used as housekeeping genes. Amplification plots were analysed using the ABI PRISM 7500 sequence detection system (Applied Biosystems) and the relative expression data were calculated by the ½ Ct method. Data analysis and functional networks Statistical analyses and graphs plotting were performed by GraphPad Prism. Statistical tests were chosen according to the sample size and variance homogeneity. The gene symbol lists resulting from the gene selection procedure and the matching gene expression values, were used to compute functional networks by using the Reactome (FI) Functional Interaction Network plugin for Cytoscape [34]. Biological processes (BP) and pathway enrichment of moduli were assessed by FDR p-value ≤0.01, while the whole network functions were computed by using FDR ≤0.1