scholarly journals Analysis of the Differential Exosomal miRNAs of DC2.4 Dendritic Cells Induced by Toxoplasma gondii Infection

2019 ◽  
Vol 20 (21) ◽  
pp. 5506
Author(s):  
Dong-Liang Li ◽  
Wei-Hao Zou ◽  
Sheng-Qun Deng ◽  
Hong-Juan Peng
Keyword(s):  
Dendritic Cells ◽  
Toxoplasma Gondii ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Biologically Active ◽  
Transferase Activity ◽  
Bioinformatics Analyses ◽  
Exosomal Mirnas

Toxoplasma gondii is an intracellular parasite that infects humans and other warm-blooded animals. Exosomes are endocytic-derived vesicles released by cells, representing an important mode of intercellular communication. In exosomes, specific molecules of proteins, lipids, and mRNAs or miRNAs have been detected, some of which are capable of transferring biologically active molecules to recipient cells. Dendritic cells (DCs) are the only antigen-presenting cells (APCs) that activate the initial immune response. In this study, high-throughput sequencing was used to analyze the exosomal miRNA profile of DC2.4 cells infected with Toxoplasma gondii for 28 h, compared with those of uninfected DC2.4 cells. Differential exosomal miRNAs (DEmiRs) from these two cell groups were analyzed. Through high-throughput sequencing, 3434 DEmiRs were obtained, and 12 stably enriched DEmiRNAs were verified by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) and selected for further analysis. The target genes of these 12 miRNAs were predicted with online analysis software and subjected to bioinformatics analyses including protein–protein interaction (PPI) network analysis, key driver analysis (KDA), gene ontology (GO) enrichment, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. These DEmiRs were found to be associated with a variety of biological processes and signaling pathways involved in host ubiquitin system, innate immunity, biosynthesis, and transferase activity and could be potential biomarkers for T. gondii infection.

scholarly journals Expression Profiling of Exosomal miRNAs Derived from the Peripheral Blood of Kidney Recipients with DGF Using High-Throughput Sequencing

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Junpeng Wang ◽  
Xin Li ◽  
Xiaoqiang Wu ◽  
Zhiwei Wang ◽  
Chan Zhang ◽  
...  
Keyword(s):  
Graft Survival ◽  
High Throughput ◽  
Peripheral Blood ◽  
Expression Profiling ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Graft Function ◽  
Molecular Regulation ◽  
Kidney Recipients ◽  
Exosomal Mirnas

Delayed graft function (DGF) is one of the major obstacles for graft survival for kidney recipients. It is profound to reduce the incidence of DGF for maintaining long-term graft survival. However, the molecular regulation of DGF is still not adequately explained and the biomarkers for DGF are limited. Exosomes are cell-derived membrane vesicles, contents of which are stable and could be delivered into recipient cells to exert their biological functions. Consequently, exosome-derived proteomic and RNA signature profiles are often used to account for the molecular regulation of diseases or reflect the conditional state of their tissue as biomarkers. Few researches have been done to demonstrate the function of exosomes associated with DGF. In this study, high-throughput sequencing was used to explore the miRNA expression profiling of exosomes in the peripheral blood of kidney recipients with DGF. We identified 52 known and 5 conserved exosomal miRNAs specifically expressed in recipients with DGF. Three coexpressed miRNAs, hsa-miR-33a-5p_R-1, hsa-miR-98-5p, and hsa-miR-151a-5p, were observed to be significantly upregulated in kidney recipients with DGF. Moreover, hsa-miR-151a-5p was positively correlated with the first-week serum CR, BUN, and UA levels of the kidney recipients after transplantation. Furthermore, we also analyzed functions and signaling pathways of the three upregulated miRNAs target genes to uncover putative mechanism of how these exosomal miRNAs functioned in DGF. Overall, these findings identified biomarker candidates for DGF and provided new insights into the important role of the exosomal miRNAs regulation in DGF.

scholarly journals Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 30
Author(s):  
Yaodong Zhao ◽  
Wenjing Ma ◽  
Xiaohong Wei ◽  
Yu Long ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Drought Stress ◽  
Medicago Sativa ◽  
High Throughput ◽  
Drought Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

Mining the Biodiversity of Plants: A Revolution in the Making

Science ◽  
2012 ◽  
Vol 336 (6089) ◽  
pp. 1658-1661 ◽  
Author(s):  
Vincenzo De Luca ◽  
Vonny Salim ◽  
Sayaka Masada Atsumi ◽  
Fang Yu
Keyword(s):  
High Throughput ◽  
Chemical Biology ◽  
High Throughput Sequencing ◽  
Well Being ◽  
Biologically Active ◽  
Plant Metabolism ◽  
New Drug ◽  
Number Of Species ◽  
Microbial Systems

Only a small fraction of the immense diversity of plant metabolism has been explored for the production of new medicines and other products important to human well-being. The availability of inexpensive high-throughput sequencing is rapidly expanding the number of species that can be investigated for the speedy discovery of previously unknown enzymes and pathways. Exploitation of these resources is being carried out through interdisciplinary synthetic and chemical biology to engineer pathways in plant and microbial systems for improving the production of existing medicines and to create libraries of biologically active products that can be screened for new drug applications.

scholarly journals Characterization of Intracellular Growth RegulatoricgRby Utilizing Transcriptomics To Identify Mediators of Pathogenesis in Shigella flexneri

2013 ◽  
Vol 81 (9) ◽  
pp. 3068-3076 ◽  
Author(s):  
Carolyn R. Morris ◽  
Christen L. Grassel ◽  
Julia C. Redman ◽  
Jason W. Sahl ◽  
Eileen M. Barry ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Diarrheal Disease ◽  
Intracellular Growth ◽  
Bioinformatics Analyses ◽  
Content Type ◽  
Regulatory Pathways

ABSTRACTShigellaspecies Gram-negative bacteria which cause a diarrheal disease, known as shigellosis, by invading and destroying the colonic mucosa and inducing a robust inflammatory response. With no vaccine available, shigellosis annually kills over 600,000 children in developing countries. This study demonstrates the utility of combining high-throughput bioinformatic methods within vitroandin vivoassays to provide new insights into pathogenesis. Comparisons ofin vivoandin vitrogene expression identified genes associated with intracellular growth. Additional bioinformatics analyses identified genes that are present inS. flexneriisolates but not in the three otherShigellaspecies. Comparison of these two analyses revealed nine genes that are differentially expressed during invasion and that are specific toS. flexneri. One gene, a DeoR family transcriptional regulator with decreased expression during invasion, was further characterized and is now designatedicgR, forintracellulargrowthregulator. Deletion oficgRcaused no difference in growthin vitrobut resulted in increased intracellular replication in HCT-8 cells. Furtherin vitroandin vivostudies using high-throughput sequencing of RNA transcripts (RNA-seq) of an isogenic ΔicgRmutant identified 34 genes that were upregulated under both growth conditions. This combined informatics and functional approach has allowed the characterization of a gene and pathway previously unknown inShigellapathogenesis and provides a framework for further identification of novel virulence factors and regulatory pathways.

scholarly journals Differentially Expressed MicroRNAs Associated with Vein Graft Restenosis in Rats

2020 ◽  
Vol 5 (1) ◽  
pp. 45-55
Author(s):  
Shuwei Wan ◽  
Hui Cao ◽  
Yubo Zhao ◽  
Yaming Guo ◽  
Chuang Li ◽  
...  
Keyword(s):  
Intimal Hyperplasia ◽  
Vein Graft ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Group Versus ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Control Group ◽  
Bioinformatics Analyses ◽  
Vein Grafts

Objective: Intimal hyperplasia is the main cause of restenosis of vein grafts after venous transplantation. MicroRNAs are considered to play a role in vein graft restenosis; however, the expression profile of microRNAs in neointima has not been reported in detail. We wanted to investigate the differentially expressed microRNAs in the restenosis of vein grafts in rats.Methods: We established a rat model for vein transplantation to explore the pathogenic roles of microRNAs during intimal hyperplasia. Hematoxylin and eosin staining was used to confirm intimal hyperplasia in the vein grafts. Changes in microRNA expression in the vein grafts were detected 3 and 14 days after surgery by sequencing, reverse transcription‐quantitative polymerase chain reaction, and bioinformatics analyses for functional annotation.Results: We detected 711 newly predicted microRNAs among all the comparisons. Among these comparisons, 437 differentially expressed microRNAs were detected in the postoperative day 3 group versus the control group, 265 were detected in the postoperative day 14 group versus the control group, and 158 were detected in the postoperative day 14 group versus the postoperative day 3 group. Pathway analysis revealed significant enrichment of target genes that mediate Wnt, mitogen-activated protein kinase, vascular smooth muscle contraction, and regulation of actin cytoskeleton signaling.Conclusion: Our results provide insight into the pathogenesis of restenosis and will help develop novel targets in the prevention and treatment of vein graft restenosis.

scholarly journals An Integrated Analysis of Cashmere Fineness lncRNAs in Cashmere Goats

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 266 ◽  
Author(s):  
Yuan Y. Zheng ◽  
Sheng D. Sheng ◽  
Tai Y. Hui ◽  
Chang Yue ◽  
Jia M. Sun ◽  
...  
Keyword(s):  
Intermediate Filament ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Differentially Expressed ◽  
Sphingolipid Metabolism ◽  
Integrated Analysis ◽  
Messenger Rnas ◽  
Bioinformatics Analyses ◽  
Anagen Phase ◽  
Cashmere Goats

Animal growth and development are regulated by long non-coding RNAs (lncRNAs). However, the functions of lncRNAs in regulating cashmere fineness are poorly understood. To identify the key lncRNAs that are related to cashmere fineness in skin, we have collected skin samples of Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) in the anagen phase, and have performed RNA sequencing (RNA-seq) approach on these samples. The high-throughput sequencing and bioinformatics analyses identified 437 novel lncRNAs, including 93 differentially expressed lncRNAs. We also identified 3,084 differentially expressed messenger RNAs (mRNAs) out of 27,947 mRNAs. Gene ontology (GO) analyses of lncRNAs and target genes in cis show a predominant enrichment of targets that are related to intermediate filament and intermediate filament cytoskeleton. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, sphingolipid metabolism is a significant pathway for lncRNA targets. In addition, this is the first report to reveal the possible lncRNA–mRNA regulatory network for cashmere fineness in cashmere goats. We also found that lncRNA XLOC_008679 and its target gene, KRT35, may be related to cashmere fineness in the anagen phase. The characterization and expression analyses of lncRNAs will facilitate future studies on the potential value of fiber development in LCG.

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