scholarly journals Selenium Treatment Enhanced Clearance of Salmonella in Chicken Macrophages (HD11)

Antioxidants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 532 ◽  
Author(s):  
Zhexi Liu ◽  
Jianwei Huang ◽  
Yijuan Nie ◽  
Izhar Qazi ◽  
Yutao Cao ◽  
...  

As an important micronutrient, selenium (Se) plays many essential roles in immune response and protection against pathogens in humans and animals, but underlying mechanisms of Se-based control of salmonella growth within macrophages remain poorly elucidated. In this study, using RNA-seq analyses, we demonstrate that Se treatment (at an appropriate concentration) can modulate the global transcriptome of chicken macrophages HD11. The bioinformatic analyses (KEGG pathway analysis) revealed that the differentially expressed genes (DEGs) were mainly enriched in retinol and glutathione metabolism, revealing that Se may be associated with retinol and glutathione metabolism. Meanwhile, Se treatment increased the number of salmonella invading the HD11 cells, but reduced the number of salmonella within HD11 cells, suggesting that enhanced clearance of salmonella within HD11 cells was potentially modulated by Se treatment. Furthermore, RNA-seq analyses also revealed that nine genes including SIVA1, FAS, and HMOX1 were differentially expressed in HD11 cells infected with salmonella following Se treatment, and GO enrichment analysis showed that these DEGs were mainly enriched in an extrinsic apoptotic signaling pathway. In summary, these results indicate that Se treatment may not only affect retinol and glutathione metabolism in macrophages, but could also inhibit salmonella-induced macrophage apoptosis via an extrinsic apoptotic signaling pathway involving SIVA1.

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Yu Wang ◽  
Huili Jiang ◽  
Hong Meng ◽  
Jing Li ◽  
XinJing Yang ◽  
...  

Major depressive disorder (MDD) is a chronic disease that adversely affects mood and cognition. In this study, we randomly divided the rats into control group (C), model group (M), fluoxetine group (F), and acupuncture group (A), used open-field test to ascertain whether acupuncture affects chronic restraint stress (CRS) induced depression-like behaviors of rats, and explored the antidepressant mechanism of acupuncture at the molecular level of transcriptome in the frontal cortex of CRS rats by RNA-sequencing (RNA-seq). According to differentially expressed genes (DEG) analysis, we identified 134, 46, and 89 response genes differentially expressed in C versus M, F versus M, and A versus M, respectively. Through Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we identified the gene sets involved in extracellular space, inflammatory response, Toll-like receptor signaling pathway, chemokine signaling pathway, and TNF signaling pathway. In this study, RNA-seq technology was used to investigate the frontal cortex genome-wide transcriptomes in depression rats under CRS, which suggested that the antidepressant effect of acupuncture is effective and has a multitarget characteristic, which may be related to amino acid metabolism and inflammatory pathways, especially the Toll-like receptor signaling pathway, TNF signaling pathway, and NF-kappa B signaling pathway.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 160-160
Author(s):  
Ahmad Faisal Karim ◽  
Anthony R. Soltis ◽  
Nadia P Ewing ◽  
Clifton L. Dalgard ◽  
Matthew D. Wilkerson ◽  
...  

The formation of pathological anti-FVIII antibodies, referred to as "inhibitors", is the most serious complication of therapeutic FVIII infusions, affecting up to one third of severe Hemophilia A (HA) patients. Intensive FVIII therapy, i.e. "Immune Tolerance Induction" (ITI), enables ~2/3 of treated patients to achieve peripheral tolerance to FVIII. FVIII inhibitor formation is a classical T-cell dependent adaptive immune response. As such, it requires help from the innate immune system. However, the roles of innate immune cells and mechanisms of inhibitor development versus immune tolerance, achieved with or without ITI therapy, are not well understood. To address these questions, we carried out temporal transcriptomics profiling of FVIII-stimulated peripheral blood mononuclear cells (PBMCs) from HA subjects with and without a current or historic inhibitor using RNA-seq. PBMCs were isolated from 40 subjects in the following groups: (A) HA with an inhibitor that resolved either following ITI or spontaneously; (B) HA with a current inhibitor; (C) HA with no inhibitor history and (D) non-HA healthy controls. PBMCs were rested overnight and then stimulated with 5 nM FVIII, and total RNA was isolated 4, 16, 24 and 48 hours following stimulation. RNA from unstimulated cells at t = 4 hrs served as a negative control. Time-series differential expression analysis was performed with DESeq2 and genes with a log likelihood ratio test FDR <0.05 and an absolute fold change >1.25 at at least one stimulation time point compared to control were deemed significant. Subjects with a resolved past inhibitor (Group A) showed differential expression of only 15 genes. In contrast, subjects with a current inhibitor (Group B) showed differential expression of 56 genes. A clustering analysis divided the temporal trajectories of Group B genes into 3 distinct clusters. Twenty-three genes were up-regulated at 16 hr and 21 genes at 48 hr post-stimulation, respectively. Interestingly, gene ontology (GO) enrichment analysis of these genes revealed enrichments for innate immune modulators, including NLRP3, TLR8, IL32, CLEC10A and COLEC12.NLRP3 and TLR8 are associated with enhanced secretion of the pro-inflammatory cytokines IL-1beta and TNF-alpha, while IL32, which has several isoforms, has been associated with both inflammatory and regulatory immune processes. Expression levels of NLRP3, TLR8, CLEC10A and IL32 transcripts were validated by real time PCR, and changes in RNA transcript abundances correlated well with the RNA-seq results. IL-32 results were validated by both RT-qPCR on an aliquot of the original RNA sample and ELISA to measure the cytokine in supernatants at t=48 hrs. HA subjects with no inhibitor history (Group C) had 195 differentially expressed genes whose temporal profiles fell into 4 distinct clusters. GO enrichment analysis revealed biological processes related to epithelial cell proliferation, responses to toxic substances, and positive/negative regulation of cytokine secretion (TNF, NQO1, PMEPA1). The non-HA healthy control subjects (Group D) also showed cellular responses to ex vivo FVIII stimulation. A total of 63 differentially regulated genes fell into 4 distinct clusters. GO analysis identified expression patterns associated with leukocyte-mediated immunity, T-cell activation, and a hypoxia response. Overall, distinct transcriptional signatures were identified for each of the four groups, providing clues as to cellular mechanisms leading to or accompanying their disparate anti-FVIII antibody responses. We are currently characterizing PBMC immune cell subsets, e.g. macrophages and CD4+ T cells, to identify specific cell types responsible for the differentially regulated genes. Cellular responses of tolerized HA subjects and healthy non-HA controls were consistent with the known immunogenicity of FVIII, including persistence of FVIII-specific CD4+ T cells even in individuals with no measurable FVIII inhibitor. The inflammatory status of HA patients suffering from an ongoing inhibitor clearly includes up-regulation of innate immune modulators, some of which may act as ongoing danger signals that influence the responses to, and eventual outcome of, ITI therapy. Disclosures Pratt: Grifols, Inc: Research Funding; Bloodworks NW: Patents & Royalties: inventor on patents related to FVIII immunogenicity.


2018 ◽  
Vol 48 (3) ◽  
pp. 1382-1396 ◽  
Author(s):  
Yu-Xiang Liao ◽  
Zhi-Ping Zhang ◽  
Jie Zhao ◽  
Jing-Ping Liu

Background/Aims: The current study aimed to investigate the role by which fibronectin 1 (FN1) influences the cell cycle, senescence and apoptosis in human glioma cells through the PI3K/ AKT signaling pathway. Methods: Differentially expressed genes (DEGs) were identified based on gene expression data (GSE12657, GSE15824 and GSE45921 datasets) and probe annotation files from Gene Expression Omnibus. The DEGs were identified in connection with gene ontology (GO) enrichment analysis and with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The positive expression of the FN1 protein was detected by immunohistochemistry. The glioma cell lines U251 and T98G were selected and assigned into blank, negative control (NC) and siRNA-FN1 groups. A dual luciferase reporter gene assay was used to investigate the effects of FN1 on transcriptional activity through the PI3K/AKT signaling pathway. An MTT assay was applied for the detection of cell proliferation, while flow cytometry was employed for cell cycle stage and cellular apoptosis detection. β-galactosidase staining was utilized to detect cellular senescence, a scratch test was applied to evaluate cell migration, and a transwell assay was used to analyze cell invasion. Western blotting and qRT-PCR methods were used to detect the protein and mRNA expression levels, respectively, of the FN1 gene and the related genes in the PI3K/AKT pathway (PI3K, AKT and PTEN), the cell cycle (pRb, CDK4 and Cyclin D1) and cell senescence (p16 and p21) among the collected tissues and cells. Results: GSE12657 profiling revealed FN1 to be the most upregulated gene in glioma. Regarding the GSE12657 and GSE15824 datasets, FN1 gene expression was higher in glioma tissues than in normal tissues. GO enrichment analysis and KEGG pathway enrichment analysis indicated that FN1 is involved in the synthesis of extracellular matrix (ECM) components and the PI3K/AKT signaling pathway. Verification was provided, indicating the role played by the FN1 gene in the regulation of the PI3K/AKT signaling pathway, as silencing the FN1 gene was found to inhibit cell proliferation, promote cell apoptosis and senescence, and reduce migration and invasion through the down-regulation of FN1 gene expression and disruption of the PI3K-AKT signaling pathway. Conclusion: The findings of this study provide evidence highlighting the prominent role played by FN1 in stimulating glioma growth, invasion, and survival through the activation of the PI3K/AKT signaling pathway.


2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Fu-Yu Hung ◽  
Chen Chen ◽  
Ming-Ren Yen ◽  
Jo-Wei Allison Hsieh ◽  
Chenlong Li ◽  
...  

Abstract In recent years, eukaryotic long non-coding RNAs (lncRNAs) have been identified as important factors involved in a wide variety of biological processes, including histone modification, alternative splicing and transcription enhancement. The expression of lncRNAs is highly tissue-specific and is regulated by environmental stresses. Recently, a large number of plant lncRNAs have been identified, but very few of them have been studied in detail. Furthermore, the mechanism of lncRNA expression regulation remains largely unknown. Arabidopsis HISTONE DEACETYLASE 6 (HDA6) and LSD1-LIKE 1/2 (LDL1/2) can repress gene expression synergistically by regulating H3Ac/H3K4me. In this research, we performed RNA-seq and ChIP-seq analyses to further clarify the function of HDA6-LDL1/2. Our results indicated that the global expression of lncRNAs is increased in hda6/ldl1/2 and that this increased lncRNA expression is particularly associated with H3Ac/H3K4me2 changes. In addition, we found that HDA6-LDL1/2 is important for repressing lncRNAs that are non-expressed or show low-expression, which may be strongly associated with plant development. GO-enrichment analysis also revealed that the neighboring genes of the lncRNAs that are upregulated in hda6/ldl1/2 are associated with various developmental processes. Collectively, our results revealed that the expression of lncRNAs is associated with H3Ac/H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex.


2021 ◽  
Vol 8 ◽  
Author(s):  
Jinxiang Wu ◽  
Zhonglu Niu ◽  
Xiaoming Lu ◽  
Xiaozhen Tang ◽  
Xuguang Qiao ◽  
...  

Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.


2021 ◽  
Author(s):  
yanni yang ◽  
yirixiati aihaiti ◽  
peng xu ◽  
haishi zheng

Abstract Purpose:To explore the potential target proteins underlying the effect of Angelicae Pubescentis Radix(APR) on rheumatoid arthritis (RA) using a network pharmacology and molecular docking approach .Methods:First, the active components and target proteins of APR and RA related disease targets were obtained from the TCMSP, Gene Card,OMIM,DisGeNET and STRING databases. Then the active ingredient target in the RA network diagram was drawn using Cytoscape 3.7.1 software. Protein-protein interaction analysis, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analyses were carried out using the STRING and David databases. The crystal structures of RA related targets were retrieved from the RCSB PDB database. Finally, the potential active compounds and their related targets were validated using molecular docking technology.Results: Five active components of Angelicae Pubescentis Radix(APR) were screened out, including ammidin, isoimperatorin, beta-sitosterol, O-acetylcolumbianetin and angelicone and 80 key targets including MAPK8,EGFR,PTGS2,CASPASE3,MTOR,SRC,KDR,MAPK1,NOS3 and MAPK14, etc were obtained. GO enrichment analysis showed that 222 biological processes, 34 cell components and 72 molecular functions were identified; KEGG analysis showed that the targets of APR in the treatment of RA were significantly enriched in pathways in cancer, the PI3K−Akt signaling pathway, Proteoglycans in cancer, osteoclast differentiation, neuroactive ligand−receptor interaction, tuberculosis,TNF signaling pathway, serotonergic synapse, Rap1 signaling pathway,cAMP signaling pathway. The results of molecular docking showed that ammidin, isoimperatorin, beta-sitosterol, O-acetylcolumbianetin and angelicone had strong affinity for PTGS2, EGFR and MAPK8.Conclusion: APR treats RA through the characteristics of multi-component, multi-target and multi-pathway regulation.


Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2420
Author(s):  
Shaokang Zhao ◽  
Tingting Chen ◽  
Xinmao Luo ◽  
Shiyi Chen ◽  
Jie Wang ◽  
...  

Cattle-yak is an excellent hybrid of cattle and yak; they are characterized by better meat quality and stronger adaptability of harsh environments than their parents. However, male sterility of cattle-yak lay restraints on the transmission of heterosis. In this study, next generation sequence technology was performed to profile the testicular tissues transcriptome (lncRNA and mRNA) of cattle, yak, and cattle-yak. We analyzed the features and functions of significant differentially expressed genes among the three breeds. There are 9 DE lncRNAs and 46 DE mRNAs with comparisons of cattle, yak, and cattle-yak. Among them, the upregulated targeting genes, such as IGF1 and VGLL3 of cattle-yak lncRNA, may be related to the derangement of spermatocyte maturation and cell proliferation. Similarly, we found that the LDOC1 gene, which is related to the process of cellular apoptosis, is overexpressed in cattle-yak. GO enrichment analysis demonstrated that the cattle-yak is lacking the regulation of fertilization (GO: 0009566), spermatogenesis process (GO: 0007283), male gamete generation process (GO: 0048232), sexual reproduction (GO: 0019953), and multi-organism reproductive process (GO: 0044703), such processes may play important and positive roles in spermatogenesis and fertilization. Furthermore, the KEGG enrichment analysis showed that the upregulated DEGs of cattle-yak most enriched in Apoptosis (ko04210) and Hippo signaling pathway (ko04390), may lead to excessively dead of cell and inhibit cell growth, resulting in obstruction of meiosis and spermatogenesis processes. This study will enable us to deeper understand the mechanism of male cattle-yak infertility.


2021 ◽  
Vol 233 ◽  
pp. 02007
Author(s):  
Dongjun Li ◽  
Denghui Wang ◽  
Shikai Yan

Objective: To explore the potential molecular mechanism of Lycii Cortex in treating type 2 diabetes mellitus (T2DM) by virtue of network pharmacology and molecular docking method. Methods: Ingredients of Lycii Cortex were collected from TCMSP and BATMAN-TCM databases, and the corresponding targets and T2DM-related targets were obtained respectively from SwissTargetPrediction and GenCards databases. Venn diagram was applied to derive the potential active components and effect targets of Lycii Cortex in the treatment of T2DM. GO enrichment analysis and KEGG pathway analysis were performed in the database of DAVID. Cytoscape 3.6.1 was used to produce the “core components-core targets” network. The molecular docking between core components and core targets was implemented through Autodock Vina. Results: Six core components and twelve core targets of Lycii Cortex in treating T2DM were identified. GO enrichment analysis and KEGG pathway analysis suggested the following signaling pathways and biological processes were involved in the treatment of T2DM by Lycii Cortex: PI3K-Akt signaling pathway, TNF signaling pathway, HIF-1 signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and peptidyl-threonine phosphorylation, the positive regulation of cyclase activity, the positive regulation of genetic expression, and lipoprotein translocation. The binding results demonstrated a relatively high affinity between core components of Lycii Cortex, including kulactone, hederagenin, scopolin, etc., and core targets, containing IL6, PPARγ, TNF, and mTOR, indicating the efficacy of Lycii Cortex in treating T2DM. Conclusion: Lycii Cortex plays a role in the treatment of T2DM with its ingredients such as kulactone, linarin, hederagenin, and scopolin regulating glycometabolism, affecting cell apoptosis and weakening inflammatory response through targets like IL6, PPARγ, TNF, and mTOR.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10794
Author(s):  
Ceyhun Bereketoglu ◽  
Gozde Nacar ◽  
Tugba Sari ◽  
Bulent Mertoglu ◽  
Ajay Pradhan

Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.


2020 ◽  
Author(s):  
Tingting Wang ◽  
Yanwen Xu ◽  
Wanli Ji ◽  
Rui An

Abstract Background: Gegen Qinlian Decoction(GQD) has been used to treat acute colitis (AC) for several years in China and it has shown good efficacy. However, the active components and target proteins of its anti-AC effects remains to be deciphered. Methods: In this study, serum pharmacochemistry and network pharmacology strategy were integrated to identify the constituents in blood and the mechanism of GQD for the treatment of AC. Ultra-performance liquid chromatography and LTQ-Orbitrap mass spectrometry(UPLC-LTQ-Orbitrap-MS) was used to identify the absorbed components of GQD in rat serum; molecular docking and compound-target network analysis were used to predict candidate targets and critical components in GQD responsible for efficacy; In addition, the Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis and Gene Ontology(GO) enrichment analysis were used to predict the related pathways and biological process respectively; Finally, the model rats with acute colitis were induced by DSS(Dextran Sulfact Sodium) in order to verify the effects and potential mechanism of baicalein, which is an important component of GQD. Results: Based on our comprehensive systematic approach, 23 components were successfully identified in rat serum after oral administration of GQD. The predicted results of molecular docking indicated that these 23 active components closely interacted with 41 protein targets associated with inflammation, immunity and enteric mucos. Among the 23 compounds identified, baicalin, baicalein, wogonoside , liquiritin and daidzin may be the most important components of GQD. Futhermore, according to GO enrichment analysis, the 41 candidate targets identified were mainly involved in two biological process, immune system process and inflammatory response. The KEGG pathway analysis revealed that 41 candidate targets were associated with 62 biological pathways, including HIF-1 signaling pathway and PI3K/Akt signaling pathway. Animal experiments found that baicalein could inhibit the activation of PI3K/Akt/HIF-1 signaling pathway and significantly reduce pro-inflammatory cytokines, such as IL-1β, IL-6, IL-8 and TNF-α to alleviate intestinal mucosal damage and achieve a therapeutic effect on AC. Conclusion: This research not only provides a novel and scientific strategy to better understand the complex mechanism of GQD, but also offers a new perspective to identify and/or discover novel active ingredients of TCM drugs.


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