scholarly journals Whole Transcriptome Analysis of Hypertension Induced Cardiac Injury Using Deep Sequencing

2016 ◽  
Vol 38 (2) ◽  
pp. 670-682 ◽  
Author(s):  
Tao-Tao Li ◽  
Xiao-Yan Li ◽  
Li-Xin Jia ◽  
Jing Zhang ◽  
Wen-Mei Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Cell Activation ◽  
Critical Role ◽  
Cardiac Injury ◽  
Interaction Network ◽  
Receptor Interaction ◽  
Rna Seq ◽  
Cardiac Inflammation ◽  
Molecular Events ◽  
Focal Adhesion Protein

Background/Aims: Hypertension plays a critical role in the cardiac inflammation and injury. However, the mechanism of how hypertension causes the cardiac injury at a molecular level remains to be elucidated. Methods: RNA-Seq has been demonstrated to be an effective approach for transcriptome analysis, which is essential to reveal the molecular constituents of cells and tissues. In this study, we investigated the global molecular events associated with the mechanism of hypertension induced cardiac injury using RNA-Seq analysis. Results: Our results showed that totally 1,801 genes with different expression variations were identified after Ang II infusion at 1, 3 and 7 days. Go analysis showed that the top 5 high enrichment Go terms were response to stress, response to wounding, cellular component organization, cell activation and defense response. KEGG pathway analysis revealed the top 5 significantly overrepresented pathways were associated with ECM-receptor interaction, focal adhesion, protein digestion and absorption, phagosome and asthma. Moreover, protein-protein interaction network analysis indicated that ubiquitin C may play a key role in the processes of hypertension-induced cardiac injury. Conclusion: Our study provides a comprehensive understanding of the transcriptome events in hypertension-induced cardiac pathology.

scholarly journals Transcriptome Profile Analysis of Mammary Gland Tissue from Two Breeds of Lactating Sheep

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 781 ◽  
Author(s):  
Hao ◽  
Zhou ◽  
Hickford ◽  
Gong ◽  
Wang ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Profile Analysis ◽  
Critical Role ◽  
Receptor Interaction ◽  
Production Traits ◽  
Rna Seq ◽  
Transcriptome Profile ◽  
Phenotypic Differences ◽  
Mammary Gland Tissue ◽  
Genetic Mechanisms

The mammary gland is a crucial tissue for milk synthesis and plays a critical role in the feeding and growth of mammalian offspring. The aim of this study was to use RNA-sequencing (RNA-Seq) technology to provide a transcriptome profile of the ovine mammary gland at the peak of lactation. Small-Tailed Han (STH) sheep (n = 9) and Gansu Alpine Merino (GAM) sheep (n = 9), breeds with phenotypic differences in milk production traits, were selected for the RNA-Seq analysis. This revealed 74 genes that were more highly expressed in the STHs than in the GAMs. Similarly, 143 genes that were expressed at lower levels in the STHs than in the GAMs, were identified. Gene ontogeny (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these differentially expressed genes (DEGs) were associated with binding and catalytic activities, hematopoietic cell lineages, oxytocin signaling pathway and neuroactive ligand–receptor interaction. This is the first study of the transcriptome profile of the ovine mammary gland in these Chinese breeds at peak lactation. The results provide for a better understanding of the genetic mechanisms involved in ovine lactation.

scholarly journals Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hong Zeng ◽  
Bao-fu Yu ◽  
Nan Liu ◽  
Yan-yan Yang ◽  
Hua-yi Xing ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Lentiviral Vector ◽  
Interaction Network ◽  
Cholinergic Receptor ◽  
Receptor Interaction ◽  
Receptor Subtype ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Cord Injury

Abstract Background Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq. Result The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons. The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane. Conclusion Knockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.

scholarly journals RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1077 ◽  
Author(s):  
Chengchuang Song ◽  
Yongzhen Huang ◽  
Zhaoxin Yang ◽  
Yulin Ma ◽  
Buren Chaogetu ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Cell Metabolism ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Control Group ◽  
Rna Seq ◽  
Angus Cattle

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

scholarly journals Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats

2019 ◽  
Author(s):  
Hong Zeng ◽  
Bao-fu Yu ◽  
Nan Liu ◽  
Yan-yan Yang ◽  
Hua-yi Xing ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Lentiviral Vector ◽  
Interaction Network ◽  
Cholinergic Receptor ◽  
Receptor Interaction ◽  
Receptor Subtype ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Cord Injury

Abstract Abstract Background Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq. Result The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons . The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane. Conclusion Knockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.

scholarly journals RNA-Seq-Based Gene Expression Pattern and Morphological Alterations in Chick Thymus during Postnatal Development

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Zhouyiyuan Xue ◽  
Abdur Rahman Ansari ◽  
Xing Zhao ◽  
Kun Zang ◽  
Yu Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Postnatal Development ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Critical Role ◽  
Gene Expression Pattern ◽  
Receptor Interaction ◽  
Rna Seq ◽  
Morphological Alterations

The thymus is a lobulated unique lymphoid immune organ that plays a critical role in the selection, development, proliferation, and differentiation of T cells. The thymus of developing chickens undergoes continued morphological alterations; however, the biomolecular and transcriptional dynamics of the postnatal thymus in avian species is not clear yet. Therefore, the thymuses from chickens at different stages of development (at weeks 0, 1, 5, 9, 18, and 27) were used in the present study. The RNA-seq method was used to study the gene expression patterns. On average, 24120819 clean reads were mapped, differentially expressed genes (DEGs) were identified on the basis of log values (fold change), including 744 upregulated and 425 downregulated genes. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are PCNA, CCNA2, CCNB2, and CDK1. Thus, the current study revealed that during postnatal development, the thymus undergoes severe atrophy. Thymus structure was damaged and gene expression changed dramatically, especially at the 27th week of age. Moreover, we found significant changes of several signaling pathways such as the cytokine-cytokine receptor interaction and cell cycle signaling pathways. Hence, it may be inferred that those signaling pathways might be closely related to the postnatal chicken thymus development.

scholarly journals Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats

2019 ◽  
Author(s):  
Hong Zeng ◽  
Bao-fu Yu ◽  
Nan Liu ◽  
Yan-yan Yang ◽  
Hua-yi Xing ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Lentiviral Vector ◽  
Interaction Network ◽  
Cholinergic Receptor ◽  
Receptor Interaction ◽  
Receptor Subtype ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Cord Injury

Abstract Abstract Background Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq. Result The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons . The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane. Conclusion Knockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.

scholarly journals Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats

2019 ◽  
Author(s):  
Hong Zeng ◽  
Bao-fu Yu ◽  
Nan Liu ◽  
Yan-yan Yang ◽  
Hua-yi Xing ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Lentiviral Vector ◽  
Interaction Network ◽  
Cholinergic Receptor ◽  
Receptor Interaction ◽  
Receptor Subtype ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Cord Injury

Abstract Abstract Background Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq. Result The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons . The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane. Conclusion Knockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.

scholarly journals Inhalation of Essential Oil from Mentha piperita Ameliorates PM10-Exposed Asthma by Targeting IL-6/JAK2/STAT3 Pathway Based on a Network Pharmacological Analysis

2020 ◽  
Vol 14 (1) ◽  
pp. 2
Author(s):  
Mi Hye Kim ◽  
Sang Jun Park ◽  
Woong Mo Yang
Keyword(s):  
Essential Oil ◽  
Signaling Pathway ◽  
Cell Activation ◽  
A549 Cells ◽  
Interaction Network ◽  
Mentha Piperita ◽  
Receptor Interaction ◽  
Pharmacological Analysis ◽  
Stat3 Signaling ◽  
Stat3 Signaling Pathway

Fine particulate matter (PM) exposure exhibits a crucial risk factor to exacerbate airway epithelial remodeling, fibrosis, and pulmonary destruction in asthma. Based on the use of essential oils from aromatic plants on pain relief and anti-inflammatory properties, we investigated the inhibitory effects of essential oil derived from the Mentha species (MEO) against asthma exposed to PM10. The MEO (0.1 v/v %) was aerosolized by a nebulizer to ovalbumin and PM10-induced asthmatic mice. Histological changes were confirmed in the lung tissues. To define the mode of action of the MEO on asthma, a protein–protein interaction network was constructed using menthol and menthone as the major components of the MEO. Cytokine expression and the JAK2/STAT3 signaling pathway were analyzed in lung epithelial A549 cells co-treated with MEO and PM10. Inhalation of MEO by nebulization inhibited respiratory epithelium hyperplasia, collagen deposition, and goblet cell activation in asthmatic mice. Through a network pharmacological analysis, cytokine–cytokine receptor interaction and JAK/STAT was expected to be underlying mechanisms of MEO on asthma. Treatment with MEO significantly reduced the IL-6 levels with a decrease in pro-inflammatory and T helper 2-specific cytokines. PM10-induced phosphorylation of JAK2 and STAT3 was significantly decreased by MEO. Collectively, MEO may have an inhibitory effect on asthma under the condition of PM10 exposure through the IL-6/JAK2/STAT3 signaling pathway.

scholarly journals Hyaluronate-CD44 Interactions Can Induce Murine B-Cell Activation

Blood ◽  
1997 ◽  
Vol 89 (8) ◽  
pp. 2901-2908 ◽  
Author(s):  
Asimah Rafi ◽  
Mitzi Nagarkatti ◽  
Prakash S. Nagarkatti
Keyword(s):  
T Cells ◽  
B Cells ◽  
B Cell ◽  
Cell Activation ◽  
Critical Role ◽  
Surface Glycoprotein ◽  
B Cell Differentiation ◽  
B Cell Activation ◽  
Cell Surface Glycoprotein ◽  
Immunodeficient Mice

Abstract CD44 is a widely distributed cell surface glycoprotein whose principal ligand has been identified as hyaluronic acid (HA), a major component of the extracellular matrix (ECM). Recent studies have demonstrated that activation through CD44 leads to induction of effector function in T cells and macrophages. In the current study, we investigated whether HA or monoclonal antibodies (MoAbs) against CD44 would induce a proliferative response in mouse lymphocytes. Spleen cells from normal and nude, but not severe combined immunodeficient mice, exhibited strong proliferative responsiveness to stimulation with soluble HA or anti-CD44 MoAbs. Furthermore, purified B cells, but not T cells, were found to respond to HA. HA was unable to stimulate T cells even in the presence of antigen presenting cells (APC) and was unable to act as a costimulus in the presence of mitogenic or submitogenic concentrations of anti-CD3 MoAbs. In contrast, stimulation of B cells with HA in vitro, led to B-cell differentiation as measured by production of IgM antibodies in addition to increased expression of CD44 and decreased levels of CD45R. The fact that the B cells were responding directly to HA through its binding to CD44 and not to any contaminants or endotoxins was demonstrated by the fact that F(ab)2 fragments of anti-CD44 MoAbs or soluble CD44 fusion proteins could significantly inhibit the HA-induced proliferation of B cells. Also, HA-induced proliferation of B cells was not affected by the addition of polymixin B, and B cells from lipopolysaccharide (LPS)-unresponsive C3H/HeJ strain responded strongly to stimulation with HA. Furthermore, HA, but not chondroitin-sulfate, another major component of the ECM, induced B-cell activation. It was also noted that injection of HA intraperitoneally, triggered splenic B cell proliferation in vivo. Together, the current study demonstrates that interaction between HA and CD44 can regulate murine B-cell effector functions and that such interactions may play a critical role during normal or autoimmune responsiveness of B cells.

scholarly journals A critical role for c‐Myc in group 2 innate lymphoid cell activation

Allergy ◽  
2020 ◽  
Vol 75 (4) ◽  
pp. 841-852 ◽  
Author(s):  
Longyun Ye ◽  
Jiexue Pan ◽  
Mingwei Liang ◽  
Muhammad Asghar Pasha ◽  
Xiaofei Shen ◽  
...  
Keyword(s):  
Lymphoid Cell ◽  
Cell Activation ◽  
Critical Role ◽  
Innate Lymphoid Cell ◽  
Group 2
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