Over-expression of the barley Phytoglobin 1 (HvPgb1) evokes leaf-specific transcriptional responses during root waterlogging.

Oxygen deprivation (hypoxia) in the root due to waterlogging causes profound metabolic changes in the aerial organs depressing growth and limiting plant productivity in barley (Hordeum vulgare L.). Genome-wide analyses in waterlogged wild type (WT) barley (cv.

Integrative analysis reveals novel associations between DNA methylation and the serum metabolome of adolescents with type 2 diabetes: A cross-sectional study.

Objective: Rates of type 2 diabetes (T2D) among adolescents are on the rise. Epigenetic changes could be associated with the metabolic alterations in adolescents with T2D.

Methods: We performed a cross sectional integrated analysis of DNA methylation data from peripheral blood mononuclear cells with serum metabolomic data from First Nation adolescents with T2D and controls participating in the Improving Renal Complications in Adolescents with type 2 diabetes through Research (iCARE) cohort study, to explore the molecular changes in adolescents with T2D.

Transcriptome Alterations of an -Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of .

Fusarium head blight caused by is a devastating disease of malting barley. Mycotoxins associated with contaminated grain can be transferred from malt to beer and pose a health risk to consumers. In western Canada, has undergone an adaptive shift from 15ADON constituency to dominance by virulent 3ADON-producers; likewise, NIV-producers have established in regions of southern United States.

Mitogen-induced transcriptional programming in human fibroblasts.

Treatment of serum-starved quiescent human cells with fetal bovine serum (FBS), epidermal growth factor (EGF), or the phorbol ester (12-O-tetradecanoylphorbol-13-acetate, TPA) activates the RAS-MAPK pathway which initiates a transcriptional program which drives cells toward proliferation. Stimulation of the RAS-MAPK pathway activates mitogen- and stress-activated kinases (MSK) 1 and 2, which phosphorylate histone H3 at S10 (H3S10ph) or S28 (H3S28ph) (nucleosomal response) located at the regulatory regions of immediate-early genes, setting in motion a series of chromatin remodeling events that result in transcription initiation. To investigate immediate-early genes regulated by the MSK, we have completed transcriptome analyses (RNA sequencing) of human normal fibroblast cells (CCD-1070Sk) stimulated with EGF or TPA ± H89, a potent MSK/PKA inhibitor.

Genome Assembly of the Canadian two-row Malting Barley cultivar AAC Synergy.

Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide.

Evaluation of variant calling tools for large plant genome re-sequencing.

Background: Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breeding, population diversity studies for eco-geographical adaption, genotyping crop germplasm collections, and others. Accurately detecting SNPs from large polyploid crop genomes such as wheat is crucial and challenging. A few variant calling methods have been previously developed but they show a low concordance between their variant calls.

Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions.

Protein arginine methyltransferase 1 (PRMT1) and the product of this enzyme (histone H4 asymmetrically dimethylated at Arg 3; H4R3me2a) are important in the establishment and maintenance of chicken and murine erythrocyte transcriptionally active chromatin. Silencing the expression of PRMT1 results in loss of acetylated histones H3 and H4 and methylated H3K4 and prevents erythropoiesis. Here, we show that H4R3me2a and the PRMT5-catalyzed histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s) locate largely to introns of expressed genes and intergenic regions, with both marks co-localizing in the chicken polychromatic erythrocyte genome.

Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley ( L.).

Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding, the genome-wide gene expression responses in roots of waterlogged barley seedlings of Yerong and Deder2 were analyzed by RNA-Sequencing.

Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules.

Background: Emerging evidence has suggested that dysbiosis of the microbiota may play vital roles in tumorigenesis. However, the interplay between the microbiome and lung cancer remains undetermined. In this study, we characterize the microbiome in the early stage of lung cancer, which presented as ground-glass nodules (GGNs).

Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes.

The major biological role of red blood cells is to carry oxygen to the tissues in the body. However, another role of the erythroid cell is to participate in the immune response. Mature erythrocytes from chickens express Toll-like receptors and several cytokines in response to stimulation of the immune system.

Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules.

Synchronous multiple ground-glass nodules (SM-GGNs) are a distinct entity of lung cancer which has been emerging increasingly in recent years in China. The oncogenesis molecular mechanisms of SM-GGNs remain elusive. We investigated single nucleotide variations (SNV), insertions and deletions (INDEL), somatic copy number variations (CNV), and germline mutations of 69 SM-GGN samples collected from 31 patients, using target sequencing (TRS) and whole exome sequencing (WES).

Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer.

Different breast cancer (BC) subtypes have unique gene expression patterns, but their regulatory mechanisms have yet to be fully elucidated. We hypothesized that the top upregulated (Yin) and downregulated (Yang) genes determine the fate of cancer cells. To reveal the regulatory determinants of these Yin and Yang genes in different BC subtypes, we developed a lasso regression model integrating DNA methylation (DM), copy number variation (CNV) and microRNA (miRNA) expression of 391 BC patients, coupled with miRNA-target interactions and transcription factor (TF) binding sites.

CuO modified vanadium-based SCR catalysts for Hg oxidation and NO reduction.

The catalytic performance of Hg oxidation over vanadium-based SCR catalysts modified by different addition amounts of CuO was investigated. All catalysts were prepared by impregnation method and characterized. The 7% Cu/VWTi exhibited high Hg oxidation as well as a desired NO removal efficiency at 280-360 °C.

Chromatin organization of transcribed genes in chicken polychromatic erythrocytes.

Transcriptional regulation is impacted by the organization of the genome into chromatin compartments and domains. We previously reported the application of a biochemical fractionation protocol to isolate highly enriched transcribed DNA from chicken polychromatic erythrocytes. In conjunction with next-generation DNA and RNA sequencing as well as chromatin immunoprecipitation-DNA sequencing, we identified all the active chromosomal compartments and determined their structural signatures in relation to expression levels.

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice.

We have previously reported the deregulatory impact of ethanol on global DNA methylation of brain-derived neural stem cells (NSC). Here, we conducted a genome-wide RNA-seq analysis in differentiating NSC exposed to different modes of ethanol exposure. RNA-seq results showed distinct gene expression patterns and canonical pathways induced by ethanol exposure and withdrawal.

Synthesis of stable and low-CO selective ε-iron carbide Fischer-Tropsch catalysts.

The Fe-catalyzed Fischer-Tropsch (FT) reaction constitutes the core of the coal-to-liquids (CTL) process, which converts coal into liquid fuels. Conventional Fe-based catalysts typically convert 30% of the CO feed to CO in the FT unit. Decreasing the CO release in the FT step will reduce costs and enhance productivity of the overall process.

Gene Expression Detection Assay for Cancer Clinical Use.

Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting.

Genes and functions from breast cancer signatures.

Background: Breast cancer is a heterogeneous disease and personalized medicine is the hope for the improvement of the clinical outcome. Multi-gene signatures for breast cancer stratification have been extensively studied in the past decades and more than 30 different signatures have been reported. A major concern is the minimal overlap of genes among the reported signatures.

Simultaneous removal of SO and NO from flue gas by wet scrubbing using a urea solution.

Nitrogen oxides (NO) and sulfur dioxide (SO) are major air pollutants, so simultaneously removing them from gases emitted during fossil fuel combustion in stationary systems is important. Wet denitrification using urea is used for a wide range of systems. Additives have strong effects on wet denitrification using urea, and different mechanisms are involved and different effects found using different additives.

Correction: Mendelian and Non-Mendelian Regulation of Gene Expression in Maize.

[This corrects the article DOI: 10.1371/journal.pgen.

The exploration of contrasting pathways in Triple Negative Breast Cancer (TNBC).

Background: Triple Negative Breast Cancers (TNBCs) lack the appropriate targets for currently used breast cancer therapies, conferring an aggressive phenotype, more frequent relapse and poorer survival rates. The biological heterogeneity of TNBC complicates the clinical treatment further. We have explored and compared the biological pathways in TNBC and other subtypes of breast cancers, using an in silico approach and the hypothesis that two opposing effects (Yin and Yang) pathways in cancer cells determine the fate of cancer cells.

Applications of Support Vector Machine (SVM) Learning in Cancer Genomics.

Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes. Herein we reviewed the recent progress of SVMs in cancer genomic studies.

Ubiquitin C-terminal hydrolase isozyme L1 is associated with shelterin complex at interstitial telomeric sites.

Background: Ubiquitin C-terminal hydrolase isozyme L1 (UCHL1) is primarily expressed in neuronal cells and neuroendocrine cells and has been associated with various diseases, including many cancers. It is a multifunctional protein involved in deubiquitination, ubiquitination and ubiquitin homeostasis, but its specific roles are disputed and still generally undetermined.

Results: Herein, we demonstrate that UCHL1 is associated with genomic DNA in certain prostate cancer cell lines, including DU 145 cells derived from a brain metastatic site, and in HEK293T embryonic kidney cells with a neuronal lineage.

HIV-1 envelope glycoprotein stimulates viral transcription and increases the infectivity of the progeny virus through the manipulation of cellular machinery.

During HIV infection, large amounts of progeny viral particles, including infectious virus and a large proportion of defective viral particles, are produced. Despite of the critical role of the infectious viruses in infection and pathogenesis in vivo, whether and how those defective viral particles, especially the virus-associated envelope glycoprotein (vEnv), would impact viral infection remains elusive. In this study, we investigated the effect of vEnv on HIV-infected T cells and demonstrated that the vEnv was able to stimulate HIV transcription in HIV-infected cells, including peripheral blood mononuclear cells (PBMCs) isolated from HIV patients.

Two Opposing Effects (Yin and Yang) Determine Cancer Progression.

In this review, we introduce a new vision of cancer describing opposing effects that control progression. Cancer is a paradigm of opposing of "Yin" and "Yang," with Yin being the effect to promote cancer and Yang that to maintain the normal state. This Yin Yang hypothesis has been used to select Yin and Yang genes to develop multigene signatures for determining prognosis in lung and breast cancer.