182 research outputs found

    A Role for the Nucleosome Assembly Proteins TAF-Iβ and NAP1 in the Activation of BZLF1 Expression and Epstein-Barr Virus Reactivation

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    <div><p>The reactivation of Epstein-Barr virus (EBV) from latent to lytic infection begins with the expression of the viral BZLF1 gene, leading to a subsequent cascade of viral gene expression and amplification of the EBV genome. Using RNA interference, we show that nucleosome assembly proteins NAP1 and TAF-I positively contribute to EBV reactivation in epithelial cells through the induction of BZLF1 expression. In addition, overexpression of NAP1 or the β isoform of TAF-I (TAF-Iβ) in AGS cells latently infected with EBV was sufficient to induce BZLF1 expression. Chromatin immunoprecipitation experiments performed in AGS-EBV cells showed that TAF-I associated with the BZLF1 promoter upon lytic induction and affected local histone modifications by increasing H3K4 dimethylation and H4K8 acetylation. MLL1, the host protein known to dimethylate H3K4, was found to associate with the BZLF1 promoter upon lytic induction in a TAF-I-dependent manner, and MLL1 depletion decreased BZLF1 expression, confirming its contribution to lytic reactivation. The results indicate that TAF-Iβ promotes BZLF1 expression and subsequent lytic infection by affecting chromatin at the BZLF1 promoter.</p></div

    Pt-Frame@Ni <i>quasi</i> Core–Shell Concave Octahedral PtNi<sub>3</sub> Bimetallic Nanocrystals for Electrocatalytic Methanol Oxidation and Hydrogen Evolution

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    PtNi<sub>3</sub> bimetallic concave octahedrons with a majority of platinum atoms deposited on the frames were synthesized in ethylene glycol solution. The high angle annular dark field scanning transmission electron microscopy (HAAD-STEM) characterizations and energy-dispersive X-ray spectroscopy (EDS) analysis reveal that the Pt frames have a thickness of less than 2 nm, which surround a nickel core thus forming a <i>quasi</i> core–shell concave octahedral nanoparticle (NP). The element-specific anisotropic growth followed by the nanoscale phase segregation and subsequent oxidation of Ni riched facets are responsible for the formation of the concave nanostructure. The PtNi<sub>3</sub> <i>quasi</i> core–shell concave octahedrons exhibit substantially enhanced electrocatalytic properties toward methanol oxidation and hydrogen evolution reaction compared with that of the commercial Pt/C, suggesting that the Ni riched Pt–Ni NPs can be used as a potential candidate for methanol oxidation reaction (MOR) or hydrogen evolution reaction (HER) catalysts with the low utilization of Pt

    Table_1_Identification of immune-related biomarkers co-occurring in acute ischemic stroke and acute myocardial infarction.XLSX

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    BackgroundAcute ischemic stroke (AIS) and acute myocardial infarction (AMI) share several features on multiple levels. These two events may occur in conjunction or in rapid succession, and the occurrence of one event may increase the risk of the other. Owing to their similar pathophysiologies, we aimed to identify immune-related biomarkers common to AIS and AMI as potential therapeutic targets.MethodsWe identified differentially expressed genes (DEGs) between the AIS and control groups, as well as AMI and control groups using microarray data (GSE16561 and GSE123342). A weighted gene co-expression network analysis (WGCNA) approach was used to identify hub genes associated with AIS and/or AMI progression. The intersection of the four gene sets identified key genes, which were subjected to functional enrichment and protein–protein interaction (PPI) network analyses. We confirmed the expression levels of hub genes using two sets of gene expression profiles (GSE58294 and GSE66360), and the ability of the genes to distinguish patients with AIS and/or AMI from control patients was assessed by calculating the receiver operating characteristic values. Finally, the investigation of transcription factor (TF)-, miRNA-, and drug–gene interactions led to the discovery of therapeutic candidates.ResultsWe identified 477 and 440 DEGs between the AIS and control groups and between the AMI and control groups, respectively. Using WGCNA, 2,776 and 2,811 genes in the key modules were identified for AIS and AMI, respectively. Sixty key genes were obtained from the intersection of the four gene sets, which were used to identify the 10 hub genes with the highest connection scores through PPI network analysis. Functional enrichment analysis revealed that the key genes were primarily involved in immunity-related processes. Finally, the upregulation of five hub genes was confirmed using two other datasets, and immune infiltration analysis revealed their correlation with certain immune cells. Regulatory network analyses indicated that GATA2 and hsa-mir-27a-3p might be important regulators of these genes.ConclusionUsing comprehensive bioinformatics analyses, we identified five immune-related biomarkers that significantly contributed to the pathophysiological mechanisms of both AIS and AMI. These biomarkers can be used to monitor and prevent AIS after AMI, or vice versa.</p

    Data_Sheet_1_Identification of immune-related biomarkers co-occurring in acute ischemic stroke and acute myocardial infarction.PDF

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    BackgroundAcute ischemic stroke (AIS) and acute myocardial infarction (AMI) share several features on multiple levels. These two events may occur in conjunction or in rapid succession, and the occurrence of one event may increase the risk of the other. Owing to their similar pathophysiologies, we aimed to identify immune-related biomarkers common to AIS and AMI as potential therapeutic targets.MethodsWe identified differentially expressed genes (DEGs) between the AIS and control groups, as well as AMI and control groups using microarray data (GSE16561 and GSE123342). A weighted gene co-expression network analysis (WGCNA) approach was used to identify hub genes associated with AIS and/or AMI progression. The intersection of the four gene sets identified key genes, which were subjected to functional enrichment and protein–protein interaction (PPI) network analyses. We confirmed the expression levels of hub genes using two sets of gene expression profiles (GSE58294 and GSE66360), and the ability of the genes to distinguish patients with AIS and/or AMI from control patients was assessed by calculating the receiver operating characteristic values. Finally, the investigation of transcription factor (TF)-, miRNA-, and drug–gene interactions led to the discovery of therapeutic candidates.ResultsWe identified 477 and 440 DEGs between the AIS and control groups and between the AMI and control groups, respectively. Using WGCNA, 2,776 and 2,811 genes in the key modules were identified for AIS and AMI, respectively. Sixty key genes were obtained from the intersection of the four gene sets, which were used to identify the 10 hub genes with the highest connection scores through PPI network analysis. Functional enrichment analysis revealed that the key genes were primarily involved in immunity-related processes. Finally, the upregulation of five hub genes was confirmed using two other datasets, and immune infiltration analysis revealed their correlation with certain immune cells. Regulatory network analyses indicated that GATA2 and hsa-mir-27a-3p might be important regulators of these genes.ConclusionUsing comprehensive bioinformatics analyses, we identified five immune-related biomarkers that significantly contributed to the pathophysiological mechanisms of both AIS and AMI. These biomarkers can be used to monitor and prevent AIS after AMI, or vice versa.</p

    Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

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    <div><p>With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat <b>(</b><i>Triticum aestivum</i> L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat.</p></div

    Average number of sequence reads per marker using 17 ng (x-axis) and 141 ng DNA (y-axis) as template.

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    <p>The top figure used touch down (TD) and the bottom figure used non-TD PCR. The arrow points to the number of reads of CNL9 marker for <i>Sr35</i>.</p

    Average number of reads per marker in non-TD (blue column) and TD PCR (red column).

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    <p>Standard errors are shown as error bars on top of columns. Samples were run using the primer combination of 8 nM and 16 nM.</p

    Risk factors for PFS in CC patients with stage IB-IIA by univariate and multiple Cox regression analysis.

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    Risk factors for PFS in CC patients with stage IB-IIA by univariate and multiple Cox regression analysis.</p

    GBMAS two-step PCR.

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    <p>The first PCR is a multiplex and amplifies the different target regions containing SNP(s). The locus-specific forward primers were tailed with an M13 sequence at the 5’-end and the reverse primers were tailed with Ion truncated P1/B sequence. The generated amplicons contains an M13 tail and Ion truncated P1/B sequence. The second PCR involves the addition of barcodes and standard Ion A adapter to the amplicons.</p
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