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Integrated analysis of accumulated data is an effective way to obtain reliable potential diagnostic molecular in gastric cancer (GC). The study aimed to identify potential lncRNAs associated with the pathogenesis and prognosis in GC. Raw noncoding RNA microarray data (GSE53137, GSE95667, and GSE111762) was downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes between GC and adjacent normal gastric tissue samples were screened by an integrated analysis of multiple gene expression profile after gene reannotation and batch normalization. Differentially expressed genes were further confirmed by the cancer genome atlas (TCGA) database. Competing endogenous RNA (ceRNA) network, survival analysis, and gene set enrichment analysis (GSEA) were extensively applied to identify hub lncRNAs and discover potential biomarkers related to diagnosis and prognosis of GC. qPCR was applied to confirm hub lncRNA expression levels in GC tissues. In total, 17 integrated differential lncRNAs were obtained after intersections of differential genes between GEO and TCGA database. Four lncRNAs (HMGA1P4, UBE2Q1-AS1, MAGI2-AS3, MIR22HG) concentrated in ceRNA network were validated by qPCR in GC tissues, which were consistent with informatics results. The clinicopathological association revealed that four lncRNAs might be effective in GC progression. Further study revealed that GC patients with lower MAGI2-AS3 expression was evidently longer than those with higher MAGI2-AS3 expression (p = 0.015). Multivariate analysis revealed MAGI2-AS3 was independently associated with overall survival in GC. GSEA showed GC samples were differentially enriched in pyrimidine metabolism, RNA degradation, cell cycle, oxidative phosphorylation etc., and most significantly enriched in ribosome pathway in MAGI2-AS3 low expression phenotype. Four lncRNAs, including HMGA1P4, UBE2Q1-AS1, MAGI2-AS3, and MIR22HG may contribute to GC development, and MAGI2-AS3 might be associated with the prognosis of GC. [ABSTRACT FROM AUTHOR]

An experiment was performed to observe the changes in Raf-1 kinase/mitogen-activated protein kinase ERK (MEK)/extracellular signal-regulated kinase (ERK) signaling pathways in cultured hippocampal neurons and its correlation with neurons apoptosis induced by intracellular zinc depletion. Cultured hippocampal neurons were exposed to a cell membrane-permeant zinc chelator TPEN (2 µM), and to TPEN plus zinc sulfate (5 µM) for 24 h. Cultures were then processed to detect neuronal viability by the methyl thiazolyl tetrazolium assay, while apoptosis rate was simultaneously observed by the flow cytometric analysis. Caspase-3, Raf-1, pMEK, pERK1/2, and pCREB protein levels were examined by Western blot assays. The viability in TPEN-incubated neurons was notably decreased, apoptosis rate and expression of caspase-3 significantly increased compared to untreated controls. The significant down-regulation of Raf/MEK/ERK signaling pathway and expression of pCREB were decreased in TPEN-treated neurons. Co-addition of zinc almost completely reversed TPEN-induced alterations described. The results demonstrated zinc-modulated apoptosis and the expression of Raf/MEK/ERK at the protein level in hippocampal neurons. It is possible that zinc depletion-induced apoptosis in cultured hippocampal neurons may be relevant to the changes of Raf/MEK/ERK signaling pathway. [ABSTRACT FROM AUTHOR]

Ascorbate peroxidase (APX) is a member of class I of the heme-containing peroxidase family. The enzyme plays important roles in scavenging reactive oxygen species for protection against oxidative damage and maintaining normal plant growth and development, as well as in biotic stress responses. In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and leaves. Real-time quantitative PCR (RT-qPCR) analysis indicated that PtrAPX transcription was induced in response to drought, salinity, high ammonium concentration, and exogenous abscisic acid treatment. These results provide important information on the phylogenetic relationships and functions of the APX gene family in P. trichocarpa. [ABSTRACT FROM AUTHOR]

• Glutamine synthetase (GOGAT) genes has not been studied in woody plants due to its long sequences. In our study, it is for the first time to characterize the members of GOGAT family in poplar by bioinformatics methods. • GS/GOGAT cycle is the key node of carbon and nitrogen metabolism. We analyzed GOGATs expression patterns responding to carbon and nitrogen treatment, providing important clues for investigating potential roles of GOGATs and exploring mechanisms in regulating C-N balance in poplar. • A new idea was proposed to discuss the evolution and function divergence among genes by analyzing the gene expression correlation coefficient, which provided a reference for gene selection in functional verification and genetic modification. Glutamate synthase (GOGAT) is a key enzyme in glutamine synthetase (GS)/GOGAT cycle and at the hub of carbon and nitrogen metabolism, catalyzing the formation of glutamate from α-oxoglutarate and glutamine. In this study, members of GOGAT family in Populus trichocarpa were identified and analyzed by bioinformatics. The four PtGOGATs were divided into two subgroups: subgroup A (Fd-GOGAT1 and Fd-GOGAT2) and subgroup B (NADH-GOGAT1 and NADH-GOGAT2). Many important elements have been identified in the promoters of different PtGOGATs , including hormone- and light-responsive elements. Meanwhile, the transcript levels of PxGOGATs were affected by light and diurnal cycle. Quantitative real-time PCR showed PxFd-GOGATs and PxNADH-GOGATs were mainly expressed in leaves and roots in Populus × xiaohei T. S. Hwang et Liang, respectively. Under elevated CO 2 , PxGOGATs were suppressed in all tissues except the stem. And PxFd-GOGATs and PxNADH-GOGATs were strongly induced by nitrogen in leaves and roots, respectively. In addition, PxGOGATs were stimulated significantly in roots in response to NH 4 +and glutamine directly. Our results provide new insights about GOGATs in poplar and their expression patterns under exogenous substances, to lay molecular basis for studying gene function and provide a reference for exploring putative roles of GOGATs in carbon–nitrogen balance. [ABSTRACT FROM AUTHOR]

Abstract: Porcine reproductive and respiratory syndrome (PRRS) is an economically important disease in swine-producing areas. Many vaccine strategies have been developed to control the disease, but none have yet been completely successful. The development of a cell line that can produce large yields of PRRSV vaccine is very necessary. In order to determine the role of Nsp2 in the replication of the highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in MARC-145 cells, we used an RNA interference-based short hairpin RNA of Nsp2 and constructed cell lines expressing the HP-PRRSV Nsp2 gene. Conserved HP-PRRSV Nsp2 sequences were used to design short interfering RNAs and test their ability to silence PRRSV transcript expression and replication in cells in vitro transfection. Nsp2, ORF7, and β-actin mRNA expression were determined using semi-quantitative real-time PCR. Infection with siRNA targeting Nsp2 was found to reduce the Nsp2 expression in MARC-145 cells infected with PRRSV. Both MARC-145-TJ Nsp2 and MARC-145-TJM Nsp2 cell lines were screened by G418, which were infected with HP-PRRSV, normal MARC-145 cells for mock, and then virus titers were calculated by TCID50 after the CPE showing up. The downregulation of Nsp2 induced a remarkable decrease in PRRSV replication, causing the reduction of structural protein. The Nsp2-targeted siRNA was found to downregulate the expression of Nsp2 in MARC-145 cells and inducing replication reduce of PRRSV in MARC-145 cells. The shRNA vectors S-1 and S-2 could effectively induce the inhibition of viral replication in MARC-145. Results showed that cells expressing the Nsp2 gene of the highly pathogenic PRRSV TJ and attenuated TJM remained stable. PRRSV replication was faster in these cells than in MARC-145 cells, especially during the early stage. This shows that Nsp2 plays a positive role in PRRSV proliferation. [Copyright &y& Elsevier]

Abstract: Hyperhomocysteinemia is a common independent risk factor for cardiovascular diseases. The promoting effect of homocysteine (Hcy) on vascular smooth muscle cell (VSMC) proliferation has been considered as one of the important pathological bases of atherosclerosis. However, the mechanism of VSMC proliferation induced by Hcy remains unclear. The present research used proteomic techniques to globally analyze the protein changes in proliferative VSMCs. After comparing the protein expression profiles of VSMCs between the Hcy-treated and non-treated groups, 11 protein spots were found altered markedly in proliferative VSMCs with expression of eight protein spots increased and three protein spots decreased. In the differentially expressed proteins, eight protein spots were identified successfully including glycolytic metabolism proteins: pyruvate kinase M2 (PKM2), triosephosphate isomerase (TPI) and aldose reductase (AR); cytoskeletal proteins: lamin C and vimentin; and three other proteins: calreticulin; similar to WDR1 protein and LIM and SH3 protein 1. The differentially expressed proteins were further validated by Western blot and confirmed by assay of enzymes'' activities and ATP content. These results may provide some clues for comprehensively understanding the mechanism of VSMC proliferation and pathogenesis of atherosclerosis induced by Hcy. [Copyright &y& Elsevier]