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To better understand the interaction between attenuated vaccines and host antiviral responses, we used bioinformatics and public transcriptomics data to analyze the immune response mechanisms of host cells after canine distemper virus (CDV) infection in Vero cells and screened for potential key effector factors. In this study, CDV-QN-1 infect with Vero cells at an MOI of 0.5, and total RNA was extracted from the cells 24 h later and reverse transcribed into cDNA. Transcriptome high-throughput sequencing perform using Illumina. The results showed that 438 differentially expressed genes were screened, of which 409 were significantly up-regulated and 29 were significantly down-regulated. Eight differentially expressed genes were randomly selected for RT-qPCR validation, and the change trend was consistent with the transcriptomics data. GO and KEGG analysis of differentially expressed genes revealed that most of the differentially expressed genes in CDV-QN-1 infection in the early stage were related to immune response and antiviral activity. The enriched signaling pathways mainly included the interaction between cytokines and cytokine receptors, the NF-kappa B signaling pathway, the Toll-like receptor signaling pathway, and the NOD-like receptor signaling pathway. This study provides a foundation for further exploring the pathogenesis of CDV and the innate immune response of host cells in the early stage of infection.

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Circular RNAs (circRNAs) are key regulatory factors with vital functions in various biological activities. However, little has been reported concerning the genetic regulation of circRNAs during rumen development in goats. The aim of this study was to identify the genome-wide expression profiles of circRNAs in the rumen of goats during fetal development and before and after weaning. Histological morphology showed that from the fetal period (days 60 and 135 of gestation) to the prepuberal period (days 60 and 150 of age) the rumen papilla developed gradually, and the thickness of the rumen muscular layer increased. A total of 11,149 circRNAs were identified in the four development stages by RNA-sequencing. From this, 1,518 were differentially expressed circRNAs (DECs). Fifty-eight DECs were up-regulated from 60 to 135 days of gestation, and 93 from day 135 of pregnancy to 30 days after birth. A large proportion (598) of DECs were down-regulated from day 135 of gestation to 30 days after birth. The expression levels of six randomly selected circRNAs were validated by qPCR, and their back-splicing junction (BSJ) sites were also confirmed. Ontology and pathway analyses revealed that the parental genes of DECs were mainly involved in the signaling pathways related to cell proliferation and apoptosis. The interaction network of circRNAs with their target miRNAs showed its involvement in cell proliferation and apoptosis signaling pathways. In conclusion, we identified the genome-wide expression profiles of circRNAs in the rumen of goats during fetal development and before and after weaning. These results provide a basis for further study on the regulatory effect of circRNAs on the development of rumen tissues.

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Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive diseases of banana. Methods to control the disease are still inadequate. The present investigation targeted expression of defense-related genes in tissue cultured banana plantlets of Fusarium resistant and susceptible cultivars after infection with biological control agents (BCAs) and Fusarium (Foc race 1). In total 3034 differentially expressed genes were identified which annotated to 58 transcriptional families (TF). TF families such as MYB, bHLH and NAC TFs were mostly up-regulated in response to pathogen stress, whereas AP2/EREBP were mostly down-regulated. Most genes were associated with plant-pathogen response, plant hormone signal transduction, starch and sucrose metabolism, cysteine and methionine metabolism, flavonoid biosynthesis, selenocompound metabolism, phenylpropanoid biosynthesis, mRNA surveillance pathway, mannose type O-glycan biosynthesis, amino acid and nucleotide sugar metabolism, cyanoamino acid metabolism, and hormone signal transduction. Our results showed that the defense mechanisms of resistant and susceptible banana cultivars treated with BCAs, were regulated by differentially expressed genes in various categories of defense pathways. Furthermore, the association with different resistant levels might serve as a strong foundation for the control of Fusarium wilt of banana.

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OBJECTIVE: To screen the differentially expressed microRNA(miRNA) in the serum of patients with occupational pneumoconiosis(hereinafter referred to as pneumoconiosis), and explore their potential target genes and related transcription factors using bioinformatics analysis. METHODS: The pneumoconiosis and miRNA related reports were searched from the Google academic website. The miRNA sequencing or high-throughput microarray data sets based on the serum samplings of pneumoconiosis patients(case group) and normal healthy individuals(control group) were selected to screen for the differentially expressed miRNAs. Serum samples of patients with occupational silicosis and healthy controls were collected, and the relative expression of miRNAs was detected by real-time fluorescence quantitative polymerase chain reaction to verify the differential expression of miRNAs. The target genes of the differentially expressed miRNAs were predicted in the database of miRWalk, analyzed by Gene Ontology(GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes(KEGG) signaling pathway prediction. The transcription factor analysis of target genes was carried out by the database for annotation. RESULTS: Seven differentially expressed miRNAs were screened out and verified. Among them, five were up-regulated and two were down-regulated. GO enrichment analysis and KEGG signaling pathway prediction showed that the up-regulated differentially expressed miRNAs were mainly related to RNA polymerase Ⅱ promoter transcription and extracellular matrix, and were mainly involved in the occurrence and development of pulmonary fibrosis through adhesion plaque, protein digestion and absorption, phosphatidylinositol 3-kinase/protein kinase B and transforming growth factor-β signaling pathways. The down-regulated differentially expressed miRNAs were mainly related to the transcription of RNA polymerase Ⅱ promoter and the activity of DNA sequence specific transcription factors, that were mainly involved in the occurrence and development of pulmonary fibrosis through the signaling pathway of related hormone release. Transcription factor annotation results showed that SMAD family member 3, proto-oncogene JUN, forkhead box O1, early growth factor 1, β-catenin and other transcription factors may have an important relationship with the occurrence and development of pneumoconiosis. CONCLUSION: The seven miRNAs were differentially expressed in the serum of patients with pneumoconiosis. These miRNAs could be used as potential biomarkers for understanding the pathogenesis, the early diagnosis and treatment pneumoconiosis.

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Ulcerative colitis (UC) is chronic, idiopathic disease that affects the colon and the rectum and the underlying pathogenesis of UC remains to be known. The clinical drugs are mainly work based on anti-inflammation and immune system. However, most of them are expensive and have severe side effects. Therefore, identification of novel targets and exploring new drugs are urgently needed. In this study, several bioinformatics approaches were used to discover key genes and further in order to explore the pathogenesis of UC. Two microarray datasets, GSE38713 and GSE9452 were selected from NCBI-Gene Expression Omnibus database. Differentially expression genes (DEGs) were identified by using LIMMA Package of R. Then, we filtered clustered candidate genes into Gene Ontology (GO) and pathway enrichment analysis with the Database for Annotation, Visualization and Integrated Discovery (DAVID), KEGG pathway based on functions and signaling pathways with significant enrichment analysis. The protein-protein interaction (PPI) network was constructed by the Search Tool for the Retrieval of Interacting Genes/ Proteins (STRING) analysis, and visualized by Cytoscape and further analyzed by Molecular Complex Detection. Lastly, 353 up-regulated and 145 down-regulated genes were than recognized. After consulting a number of references and network degree analysis, four hub genes, namely FCGR2A, C3, INPP5A, and ACAA1 were identified, and these genes were mainly enriched in complement and coagulation cascades, mineral absorption, and Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathways. In conclusion, this study would provide new clues for the pathogenesis and identification of drug targets of UC in the near future.

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Protein N-glycosylation plays an essential role on cancers and other pathological processes. Its structural and functional studies rely on complete qualitative and quantitative information. Thus, it is important to quantify differentially expressed intact N-glycopeptides (DEGPs) at their molecular level. Here we report our application of stable isotopic diethyl labeling (SIDE) of amino groups for relative quantitation of intact N-glycopeptides. The amino groups from both the N-terminal and lysine residues of N-glycopeptides were diethylated with XH3XHO (X = 13C or C) and NaBH3CN. A linear quantitation dynamic range up to 50-fold was obtained with R2 = 0.9985 with intact N-glycopeptides from standard glycoprotein ribonuclease B (RNase B). In proof-of-principle comparative N-glycoproteomics study of aberrant N-glycosylation of gastric cancer tissues vs. adjacent tissues using SIDE, 644 DEGPs (≥1.5-fold change, p < 0.05, p was calculated using t-test) were discovered. With its accuracy and big dynamic range, SIDE can be applied to quantitative study of any aberrant glycosylation at the intact glycopeptide level.

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Hepatocellular carcinoma (HCC) accounts for approximately 85-90% of all liver cancer cases and has poor relapse-free survival. There are many gene expression studies that have been performed to elucidate the genetic landscape and driver pathways leading to HCC. However, existing studies have been limited by the sample size and thus the pathogenesis of HCC is still unclear. In this study, we performed an integrated characterization using four independent datasets including 320 HCC samples and 270 normal liver tissues to identify the candidate genes and pathways in the progression of HCC. A total of 89 consistent differentially expression genes (DEGs) were identified. Gene-set enrichment analysis revealed that these genes were significantly enriched for cellular response to zinc ion in biological process group, collagen trimer in the cellular component group, extracellular matrix (ECM) structural constituent conferring tensile strength in the molecular function group, protein digestion and absorption, mineral absorption and ECM-receptor interaction. Network system biology based on the protein-protein interaction (PPI) network was also performed to identify the most connected and important genes based on our DEGs. The top five hub genes including osteopontin (SPP1), Collagen alpha-2(I) chain (COL1A2), Insulin-like growth factor I (IGF1), lipoprotein A (LPA), and Galectin-3 (LGALS3) were identified. Western blot and immunohistochemistry analysis were employed to verify the differential protein expression of hub genes in HCC patients. More importantly, we identified that these five hub genes were significantly associated with poor disease-free survival and overall survival. In summary, we have identified a potential clinical significance of these genes as prognostic biomarkers for HCC patients who would benefit from experimental approaches to obtain optimal outcome.

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BACKGROUND: Mud crab, Scylla paramamosain, a euryhaline crustacean species, mainly inhabits the Indo-Western Pacific region. Wild mud crab spawn in high-salt condition and the salinity reduced with the growth of the hatching larvae. When the larvae grow up to megalopa, they migrate back to estuaries and coasts in virtue of the flood tide, settle and recruit adult habitats and metamorphose into the crablet stage. Adult crab can even survive in a wide salinity of 0-35 ppt. To investigate the mRNA profile after salinity stress, S. paramamosain megalopa were exposed to different salinity seawater (low, 14 ppt; control, 25 ppt; high, 39 ppt). RESULTS: Firstly, from the expression profiles of Na+/K+/2Cl- cotransporter, chloride channel protein 2, and ABC transporter, it turned out that the 24 h might be the most influenced duration in the short-term stress. We collected megalopa under different salinity for 24 h and then submitted to mRNA profiling. Totally, 57.87 Gb Clean Data were obtained. The comparative genomic analysis detected 342 differentially expressed genes (DEGs). The most significantly DEGs include gamma-butyrobetaine dioxygenase-like, facilitated trehalose transporter Tret1, sodium/potassium-transporting ATPase subunit alpha, rhodanese 1-like protein, etc. And the significantly enriched pathways were lysine degradation, choline metabolism in cancer, phospholipase D signaling pathway, Fc gamma R-mediated phagocytosis, and sphingolipid signaling pathway. The results indicate that in the short-term salinity stress, the megalopa might regulate some mechanism such as metabolism, immunity responses, osmoregulation to adapt to the alteration of the environment. CONCLUSIONS: This study represents the first genome-wide transcriptome analysis of S. paramamosain megalopa for studying its stress adaption mechanisms under different salinity. The results reveal numbers of genes modified by salinity stress and some important pathways, which will provide valuable resources for discovering the molecular basis of salinity stress adaptation of S. paramamosain larvae and further boost the understanding of the potential molecular mechanisms of salinity stress adaptation for crustacean species.

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Although the influenza A virus H7N9 subtype circulates within several avian species, it can also infect humans with a severe disease outcome. To better understand the biology of the H7N9 virus we examined the host response to infection in avian and human cells. In this study we used the A/Anhui/1/2013 strain, which was isolated during the first wave of the H7N9 epidemic. The H7N9 virus-infected both human (Airway Epithelial cells) and avian (Chick Embryo Fibroblast) cells, and each infected host transcriptome was examined with bioinformatic tools and compared with other representative avian and human influenza A virus subtypes. The H7N9 virus induced higher expression changes (differentially regulated genes) in both cell lines, with more prominent changes observed in avian cells. Ortholog mapping of differentially expression genes identified significant enriched common and cell-type pathways during H7N9 infections. This data confirmed our previous findings that different influenza A virus subtypes have virus-specific replication characteristics and anti-virus signaling in human and avian cells. In addition, we reported for the first time, the new HIPPO signaling pathway in avian cells, which we hypothesized to play a vital role to maintain the antiviral state of H7N9 virus-infected avian cells. This could explain the absence of disease symptoms in avian species that tested positive for the presence of H7N9 virus.

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Virulent morbillivirus infections, including Meals Virus (MeV) and Canine Distemper Virus (CDV), caused severe immune suppression and leukopenia, while attenuated vaccine strains developed protective host immune responses. However, the detailed molecular foundations of host antiviral responses were poorly characterized. In order to better understand the interactions between attenuated vaccine and host antiviral responses, the global gene expression changes in CDV-11-infected DH82 cells, a macrophage-derived cell line from canine, were investigated by transcriptomic analysis, and portions of results were confirmed with quantitative RT-PCR. The results exhibited that 372 genes significantly up-regulated (p < .01) and 119 genes were significantly down-regulated (p < .01) in CDV-infected macrophages DH82 at 48 h p.i.. The enriched functions of the significantly up-regulated (p < .01) genes were closely associated with interferon stimulated genes (ISGs), chemokine genes and pro-inflammatory factor genes. Gene ontology and pathway analysis of differentially expressed genes (DEGs) revealed that the most significantly involved pathways in CDV-infected DH82 cells were NF-κB and TNF signaling pathway, cytokine-cytokine receptor interaction, and pathogen associated molecular patterns (PAMPs), such as Toll-like, RIG-I-like and NOD-like receptor signalings. Thus, the findings indicated that pattern recognition receptors (PRRs) possibly mediated host innate and protective antiviral immune responses in CDV-11 infected DH82 cells.

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Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.

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In this study, we identified and characterized a tripartite motif containing 25 (TRIM25) gene homologue, LcTRIM25, from large yellow croaker (Larimichthys crocea). Two isoforms of LcTRIM25, which were generated via alternative splicing, were identified via a molecular analysis of cDNA clones. The long isoform of LcTRIM25 (termed as LcTRIM25-L) contained the full open reading frame of the gene, encoded a protein of 698 amino acid residues, and possessed 11 exons. The short isoform of LcTRIM25 (termed as LcTRIM25-S) contained 9 exons and encoded a protein of 665 amino acid residues. The two LcTRIM25 isoforms contained a conserved Really Interesting New Gene (RING) domain, a B-box2 domain, a Coiled-coil domain (CCD), and variable C-terminal PRY/SPRY domains. Phylogenetic analysis showed that the two LcTRIM25 isoforms of the large yellow croaker was clustered together with their counterparts from other teleost fish. The Real-time PCR analysis showed that the LcTRIM25-L and LcTRIM25-S isoforms were both ubiquitously expressed in nine examined tissues in the large yellow croaker, with predominant expressions in the liver. The expression levels of the two isoforms of LcTRIM25 were rapidly and significantly upregulated in vivo after poly (I:C) stimulation in peripheral blood, head kidney, spleen and liver. Moreover, LcTRIM25-L and LcTRIM25-S showed differential expression post poly(I:C) stimulation. LcTRIM25 may have a dual role in innate immunity via alternative gene splicing. These results indicated that LcTRIM25 is likely to be involved in antiviral immune responses.

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The melanoma is one of the most dangerous forms of skin diseases. It may spread to other parts of the body and cause serious illness and death. Early detection and diagnosis are crucial. However, the systemic expression analysis for the different staging of melanoma is still lacking to date. In this study, we analyzed the gene expression profiles of the different staging of melanoma by the differential expression analysis and random forest analysis. First, the results of the principal component analysis showed that the clustering of primary tumor samples, normal samples, and pigment nevus samples got closer, while the clustering of tumor metastatic samples and normal samples was far away. Moreover, the gene expression of tumor metastasis stage and the initial stage had obvious differences. Almost 426 genes identified had differential expression. The functional enrichment of differentially expressed genes was associated with the epidermal cell differentiation, epidermis development, and the keratinocyte differentiation. Taken together, our findings identified the differentially expressed signatures between primary melanoma and metastatic melanoma. Our results would provide the potential mechanisms of melanoma.

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Gestational diabetes mellitus (GDM) is becoming a growing threat for all pregnancies. In this study, we set up an automatic screening method combining both transcriptomic databases and support vector machine (SVM)-based pattern recognition to select biomarkers that can be used in predicting and preventing GDM for gravidas. We screened 63 samples (32 GDM samples and 31 normal controls) in GEO database for the GDM-specific biomarkers. Differentially expressed genes between patients with GDM and normal controls were picked out using edgeR package. Enrichment analysis was performed using database for annotation, visualization, and integrated discovery. The regulatory gene network was constructed based on the KEGG pathway database. Genes in the hub of the network were selected as specific biomarkers of GDM and further validated through document investigation. Finally, the GDM prediction model was verified using the SVMs. In total, 189 probes corresponding to 69 genes that differentially expressed between GDM and controls were screened out by edgeR package. Nineteen pathways were clustered by KEGG enrichment analysis and were integrated into a regulatory network containing 572 nodes and 1874 edges. The intersection of 50 hub genes extracted from the network and 69 differential genes picked out by edgeR was a collection of six genes, including members of HLA superfamily. In the SVM model, the six genes had a good capacity of predicting GDM in both the training data set (area under curve [AUC] is 0.781) and the testing data set (AUC is 0.710) and had been reported to be associated with GDM. We found that the collection of six genes can be potentially applied as a biomarker for GDM diagnosis.

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BACKGROUND: We aimed to explore potential molecular basis of keloid formation and response mechanism of keloid to hydrocortisone (HC). METHODS: Transcriptional profile of GSE7890 which contained five normal scars with no HC treatment (NNHC), four normal scars treated with HC (NHC), five keloids with no HC treatment (KNHC), and five keloids treated with HC (KHC) samples was downloaded to identify differentially expressed genes (DEGs). Based on DEGs, hierarchical cluster analysis and pathway enrichment analysis were performed. Then, identification of characteristic pathway was performed, followed by calculation of pathway deviation score. RESULTS: Compared to NNHC group, total 1603 DEGs in NHC group, 895 DEGs in KHC group, and 832 DEGs in KNHC group were identified. Hierarchical cluster analysis revealed these four groups could be well distinguished. Total three pathways included cytokine-cytokine receptor interactions were significantly different between KNHC and NNHC groups. Besides, MAPK signaling pathway, endocytosis, and apoptosis were selected between KHC and KNHC groups. Genes of vascular endothelial growth factor C (VEGFC), tenascin C (TNC), and jun proto-oncogene (JUN) were selected as important DEGs in KHC, KNHC, and NHC groups, respectively. CONCLUSIONS: VEGF and TNC were, respectively, involved in KHC and KNHC in the mechanism of focal adhesion. JUN might be a potential molecular marker related to normal scar.

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Long noncoding RNAs (lncRNAs) may play widespread roles in various biological processes. However, systematic profiles of lncRNAs in the biological responses of Pacific Oyster (Crassostrea gigas) to pathogen infection have not yet been demonstrated. Here, we have conducted an exhaustive comparative transcriptome analysis using a bioinformatics approach to exam the functions of lncRNAs response to Ostreid herpesvirus 1µVar (OsHV-1µVar) challenge. In total, 101 differentially expressed lncRNAs (DE-lncRNA) during OsHV-1µVar infections were identified. Compared with differentially expressed mRNAs (DE-mRNA), DE-lncRNAs are shorter in terms of overall length but longer in terms of exon length. These lncRNAs shared similar characteristics with previously reported invertebrate lncRNAs, such as relatively low GC content, low exon number and low sequence conservation, but low expression level were not observed. 20 DE-lncRNAs are typically co-expressed with their neighboring genes annotated as GO terms (GO: 0044237), indicating that these lncRNAs are involved in binding and cellular process functions in cis mode. The weighted gene co-expression network (WGCNA) analysis resulted in 15 modules. The highlighted blue module was specifically demonstrated a co-expression relationship between 14 DE-lncRNAs and 17 immune-related DE-mRNAs (IR-DE-mRNA). Three hub lncRNAs within this module were co-expressed with one hub IR-DE-mRNA involved in fibrinogen-related protein. It was speculated that lncRNAs is extensively involved in oyster antiviral innate immune system. The present study will facilitate subsequently experimental studies to unravel the function of lncRNAs in marine invertebrate response to pathogen infection.

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MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although animal miRNAs have been extensively studied in model systems, less is known in other animal with limited genome sequence data, including Chinese giant salamander (Andrias davidianus). The identification of the full repertoire of miRNAs expressed in the liver, spleen and muscle of A. davidianus would significantly increase our understanding for physiological function of A. davidianus, in this ancient and endangered urodele amphibian. In this study, three independent small RNA libraries were constructed from the liver, spleen and muscle of A. davidianus. The libraries were subjected to high-throughput sequencing by using the Illumina deep sequencing. As a result, a total of 12,831,239, 13,592,195 and 9,887,531 raw reads representing 2,240,771, 1,363,266 and 1,964,252 clean reads per library were obtained separately. Through bioinformatics analysis, we identified total of 553 known miRNAs and 44 putative novel miRNAs in our small RNA dataset from liver, spleen and muscle tissues. Five known miRNAs (gga-miR-10a-5p, pma-miR-29d-5p, aca-miR-338-3p, hsa-miR-455-3p and ssa-miR-2184-5p_R-1) and three novel miRNAs (PC-5p-891_1763, PC-5p-32538_50 and PC-3p-33645_48) showed different expression in eight different tissues as revealed by stem-loop qPCR analysis. This study characterized the miRNA of A. davidianus for the first time, which provides an opportunity for further understanding of miRNA regulation function in A. davidianus ranked as living fossils.

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Our study aimed to explore long non-coding RNAs (lncRNAs) contributing to the development of bladder cancer, as well as to identify more critical DEGs and lncRNAs that would characterize low- and high-grade bladder cancer. The microarray data of GSE55433 was downloaded from Gene Expression Omnibus database, including 57 urothelial cancer samples (23 low-grade NMI, 14 high-grade NMI and 20 invasive tumors) and 26 normal controls. The differentially expressed genes (DEGs) and differentially expressed lncRNAs were identified in 3 groups (low-grade NMI vs. normal, high-grade NMI vs. normal and invasive UC vs. normal). Functional enrichment analysis was performed upon the DEGs in different groups. Besides, protein-protein interaction (PPI) network was constructed based on common DEGs and remaining DEGs in each group. Co-expression analysis was performed to identify the co-expressed DEG-lncRNAs pairs. Different number of DEGs and differentially expressed lncRNAs were respectively identified from those 3 groups. NONHSAG013805 (down-regulated) and NONHSAG009271 (down-regulated) were common lncRNAs. NONHSAG013805 was connected with the down-regulated gene EIF3E and NONHSAG009271 was linked to MYL12A (down-regulated). Moreover, NONHSAG034203 (up-regulated) was co-expressed with ADM5 (up-regulated) in low-grade NMI cancer, while the down-regulated NONHSAG045391 was connected with the down-regulated DEGs DAD1 and STUB1 in high-grade NMI cancer and invasive bladder cancer. Our study indicates that NONHSAG013805 and NONHSAG009271 may play key roles in bladder cancer via co-expressing with EIF3E and MYL12A, respectively. Moreover, NONHSAG034203 may be involved in low-grade NMI bladder cancer via targeting ADM5, while NONHSAG045391 may contribute to high-grade NMI and invasive bladder cancer via targeting DAD1 and STUB1.

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Tuber mustard (Brassica juncea (L.) Czern. et Coss. var. tumida Tsen et Lee) is an important vegetable crop with a characteristic of expanded stem that is edible. The underlying molecular mechanism of the stem expansion is not well understood. Here, we reported that a total of 51 differentially expressed fragments (DEFs) with three expression patterns during stem expansion of tuber mustard were identified by cDNA-AFLP analysis. Among the DEFs, DEF11 with high homology to Arabidopsis thaliana apyrase 2 (AtAPY2) that encodes an enzyme with ATPase and ADPase activity was development- and tissue-specific. DEF11 was thus renamed as BjAPY2. The expression levels of BjAPY2 increased with the stem expression and were the highest at stage IV, a developmental stage at which the stem expanded most rapidly. In contrast, the BjAPY2 expression levels in leaves were much lower and remained unchanged during leaf development and expansion, suggesting that BjAPY2 was closely associated with the expansion of stems but not of leaves in the tuber mustard. Interestingly, the expression of BjAPY2 was higher in the mustard under short-day (SD) photoperiod (8 h/16 h) than that under long-day (LD) photoperiod (16 h/8 h); similarly, the transcript levels of BjAPY2 were higher in the mustard grown at low temperature (14 °C/12 °C) than that at high temperature (26 °C /24 °C). The SD photoperiod and low temperature were two environmental conditions that favored the mustard stem expansion. Further cloning and analysis of the promoter region of BjAPY2 revealed that there were indeed several types of motifs in the promoter region, including the light and temperature responsive elements. These results suggested that BjAPY2 might play an important role during the stem expansion of the tuber mustard.

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BACKGROUND: MicroRNAs (miRNAs) play important roles in regulating gene expression of plants, animals and viruses. Comprehensive characterization of host and viral miRNA will help uncover the molecular mechanisms that underlie the progression of human cytomegalovirus (HCMV) latent infection. To investigate the miRNA expression profile of HCMV and host cells during latent infection, we performed deep-sequencing analysis of the small RNAs isolated from HCMV-infected and mock-infected human monocytic leukemia cell line, THP-1. RESULTS: We established a HCMV latent infection cell model using the THP-1 cells. High-throughput sequencing technology was used to sequence small RNA libraries of the HCMV-infected and mock-infected THP-1 and to investigate their small RNA transcriptomes. We found eight miRNAs including miR-US25-1, miR-US25-2-5p and miR-UL112 that were expressed by HCMV during latent infection. The expressions of the host miRNAs were also affected by HCMV latent infection. At least 49 cellular miRNAs were differentially expressed: 39 were up-regulated and 10 were down-regulated upon HCMV latent infection. The expression of the human miRNA hsa-miR-124-3p was significantly up-regulated in the HCMV latent infection library. In addition, we found 14 cellular novel miRNAs in the HCMV-infected and mock-infected THP-1 libraries. Functional annotation of the target genes of the differentially expressed miRNAs suggested that the majority of the genes are involved in melanogenesis, pathways in cancer, endocytosis and wnt signaling pathway. CONCLUSIONS: The small RNA transcriptomes obtained in this study demonstrate the usefulness of the deep-sequencing combined with bioinformatics approach in understanding of the expression and function of host and viral small RNAs in HCMV latent infection. This approach can also be applied to the study of other kinds of viruses.

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