scholarly journals Comparative transcriptome analysis of the swimbladder reveals expression signatures in response to low oxygen stress in channel catfish,Ictalurus punctatus

2018 ◽  
Vol 50 (8) ◽  
pp. 636-647 ◽  
Author(s):  
Yujia Yang ◽  
Qiang Fu ◽  
Xiaozhu Wang ◽  
Yang Liu ◽  
Qifan Zeng ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Ictalurus Punctatus ◽  
Channel Catfish ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Mapk Signaling ◽  
Hypoxia Tolerance ◽  
Economic Losses ◽  
Ras Signaling ◽  
Low Oxygen

Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been considered as an accessory respiration organ surrounded by a dense capillary countercurrent exchange system. In this regard, we conducted RNA-Seq analysis with swimbladder samples of catfish under hypoxic and normal conditions to determine if swimbladder was responsive to low oxygen treatment and to reveal genes, their expression patterns, and pathways involved in hypoxia responses in catfish. A total of 155 differentially expressed genes (DEGs) were identified from swimbladder of adult catfish, whereas a total of 2,127 DEGs were identified from swimbladder of fingerling catfish under hypoxic condition as compared with untreated controls. Subsequent pathway analysis revealed that many DEGs under hypoxia were involved in HIF signaling pathway ( nos2, eno2, camk2d2, prkcb, cdkn1a, eno1, and tfrc), MAPK signaling pathway (voltage-dependent calcium channel subunit genes), PI3K/Akt/mTOR signaling pathway ( itga6, g6pc, and cdkn1a), Ras signaling pathway ( efna3 and ksr2), and signaling by VEGF ( fn1, wasf3, and hspb1) in catfish swimbladder. This study provided insights into regulation of gene expression and their involved gene pathways in catfish swimbladder in response to low oxygen stresses.

scholarly journals Identification and Characterization of MAPK Signaling Pathway Genes and Associated lncRNAs in the Ileum of Piglets Infected by Clostridium perfringens Type C

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Ruirui Luo ◽  
Xiaoyu Huang ◽  
Zunqiang Yan ◽  
Xiaoli Gao ◽  
Pengfei Wang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Clostridium Perfringens ◽  
Expression Patterns ◽  
Strong Support ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Sequencing Data ◽  
Type C

Clostridium perfringens type C (C. perfringens type C) is one of the main microbial pathogens responsible for piglet diarrhea worldwide, causing substantial economic losses for pig-rearing industries. The mitogen-activated protein kinase (MAPK) signaling pathway is a key regulator of inflammatory bowel disease, especially necrotic enteritis. However, whether and how the MAPK signaling pathway is involved in regulating the process of piglet diarrhea when challenged by C. perfringens type C are still unknown. Here, we screened 38 differentially expressed genes (DEGs) in piglets’ ileum tissues experimentally infected with C. perfringens type C that were enriched in the Sus scrofa MAPK signaling pathway, based on our previous transcriptome data. Of these DEGs, 12 genes (TRAF2, MAPK8, and GADD45G, among others) were upregulated whereas 26 genes (MAPK1, TP53, and CHUK, among others) were downregulated in the infected group. Our results showed that MAPK1, TP53, MAPK8, MYC, and CHUK were in the core nodes of the PPI network. Additionally, we obtained 35 lncRNAs from the sequencing data, which could be trans-targeted to MAPK signaling pathway genes and were differentially expressed in the ileum tissues infected with C. perfringens. We used qRT-PCR to verify the expression levels of genes and lncRNAs related to the MAPK signaling pathway; their expression patterns were consistent with RNA sequencing data. Our results provide strong support for deeply exploring the role of the MAPK signaling pathway in diarrhea caused by C. perfringens type C.

scholarly journals Ovary-derived circular RNAs profile analysis during the onset of puberty in gilts

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiangchun Pan ◽  
Wentao Gong ◽  
Yingting He ◽  
Nian Li ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Signaling Pathway ◽  
Gene Networks ◽  
Profile Analysis ◽  
Mirna Gene ◽  
Mapk Signaling ◽  
Circular Rnas ◽  
Ras Signaling ◽  
Female Reproduction ◽  
Non Coding Rna

Abstract Background In mammals, the ovary is the essential system of female reproduction for the onset of puberty, and the abnormal puberty has negative outcomes on health. CircRNA is a non-coding RNA produced by non-canonical alternative splicing (AS). Several studies have reported that circRNA is involved in the gene regulation and plays an important role in some human diseases. However, the contribution of circRNA has received little known within the onset of puberty in ovary. Results Here, the profiles of ovarian circRNAs across pre-, in- and post-pubertal stages were established by RNA-sEq. In total, 972 circRNAs were identified, including 631 stage-specific circRNAs and 8 tissue-specific circRNAs. The biological functions of parental genes of circRNAs were enriched in steroid biosynthesis, autophagy-animal, MAPK signaling pathway, progesterone-mediated oocyte maturation and ras signaling pathway. Moreover, 5 circRNAs derived from 4 puberty-related genes (ESR1, JAK2, NF1 and ARNT) were found in this study. The A3SS events were the most alternative splicing, but IR events were likely to be arose in post-pubertal ovaries. Besides, the circRNA-miRNA-gene networks were explored for 10 differentially expressed circRNAs. Furthermore, the head-to-tail exon as well as the expressions of 10 circRNAs were validated by the divergent RT-qPCR and sanger sequencing. Conclusions In summary, the profiles of ovarian circRNAs were provided during pubertal transition in gilts, and these results provided useful information for the investigation on the onset of puberty at the ovarian-circRNAs-level in mammals.

Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

2020 ◽  
Author(s):  
Tao Zhong ◽  
Cheng Wang ◽  
Jiangtao Hu ◽  
Xiaoyong Chen ◽  
Lili Niu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Target Genes ◽  
Genetic Regulation ◽  
Mapk Signaling ◽  
Regulation Mechanism ◽  
Ras Signaling ◽  
Genome Wide ◽  
A Genome ◽  
Differentially Expressed Mirnas ◽  
And Function

Abstract Background: Rumen is an important digestive organ of ruminant. From fetal to adult stage, the morphology, structure and function of rumen have changed significantly. But the intrinsic genetic regulation is still limited. We previously reported a genome-wide expression profile of miRNAs in prenatal goat rumens. In the present study, we rejoined analyzed the transcriptomes of rumen miRNAs during prenatal (E60 and E135) and postnatal (D30 and D150) stages.Results: A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the preweaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites between miR-148a-3p and QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI was observed not in intestinal tracts but in rumen tissues by in situ hybridization. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers, suggesting that miR-148a-3p involve in the development of rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells.Conclusions: Taken together, these results identified the DEMs involved in the development of rumen and provided an insight into the regulation mechanism of goat rumens during development.

scholarly journals A Preliminary Study on the Characteristics of microRNAs in Ovarian Stroma and Follicles of Chuanzhong Black Goat during Estrus

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 970
Author(s):  
Tingting Lu ◽  
Xian Zou ◽  
Guangbin Liu ◽  
Ming Deng ◽  
Baoli Sun ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Mapk Signaling ◽  
Functional Enrichment ◽  
Small Rna Sequencing ◽  
Follicular Maturation ◽  
Ovarian Stroma

microRNAs (miRNAs) play a significant role in ovarian follicular maturity, but miRNA expression patterns in ovarian stroma (OS), large follicles (LF), and small follicles (SF) have been rarely explored. We herein aimed to identify miRNAs, their target genes and signaling pathways, as well as their interaction networks in OS, LF, and SF of Chuanzhong black goats at the estrus phase using small RNA-sequencing. We found that the miRNA expression profiles of LF and SF were more similar than those of OS—32, 16, and 29 differentially expressed miRNAs were identified in OS vs. LF, OS vs. SF, and LF vs. SF, respectively. Analyses of functional enrichment and the miRNA-targeted gene interaction network suggested that miR-182 (SMC3), miR-122 (SGO1), and miR-206 (AURKA) were involved in ovarian organogenesis and hormone secretion by oocyte meiosis. Furthermore, miR-202-5p (EREG) and miR-485-3p (FLT3) were involved in follicular maturation through the MAPK signaling pathway, and miR-2404 (BMP7 and CDKN1C) played a key role in follicular development through the TGF-β signaling pathway and cell cycle; nevertheless, further research is warranted. To our knowledge, this is the first study to investigate miRNA expression patterns in OS, LF, and SF of Chuanzhong black goats during estrus. Our findings provide a theoretical basis to elucidate the role of miRNAs in follicular maturation. These key miRNAs might provide candidate biomarkers for the diagnosis of follicular maturation and will assist in developing new therapeutic targets for female goat infertility.

scholarly journals Bioinformatics analysis reveals different gene expression patterns in chondrocytes from knee and finger joints: implications for the effect of mechanical stress in the osteoarthritic development

2020 ◽  
Author(s):  
Wei Mei ◽  
Songjiang Yin ◽  
Xiaoqing Shi ◽  
Xiaochen Li ◽  
Li Zhang ◽  
...  
Keyword(s):  
Cell Division ◽  
Mechanical Stress ◽  
Signaling Pathway ◽  
Expression Patterns ◽  
Significant Risk ◽  
Mitotic Checkpoint ◽  
Mapk Signaling ◽  
Positive Regulation ◽  
Finger Joints ◽  
Apoptotic Process

Abstract Background Mechanical stress has been well known to be a significant risk factor for the onset and progression of osteoarthritis (OA). The objective of this study is to clarify the key genes and the signaling pathways which is associated with the effect of mechanical stress on OA development. Results A total of 213 Differentially expressed genes (DEGs) were identified in cultured chondrocytes from knee and finger joints, including 101 up- and 112 down-regulated genes, which brought an enrichment in positive or negative regulation of cell proliferation, positive regulation of cell division, positive regulation of apoptotic process and embryonic limb morphogenesis. Two comparison cohorts shared 122 overlapping genes including 49 up- and 73 down-regulated genes, which enriched in DNA replication, cell division, calcium ion binding and positive regulation of apoptotic process. Twelve hub overlapped genes including Cyclin dependent kinase 1 (CDK1), Kinesin family member 11 (KIF11), Mitotic checkpoint serine/threonine kinase (BUB1) and Mitotic arrest deficient 2 like 1 (MAD2L1) were defined and predicted miRNAs of the genes mainly enriched in Transforming growth factor beta (TGF-β) signaling pathway, Wnt signaling pathway and Mitogen activated kinase-like protein (MAPK) signaling pathway. Conclusions Mechanical stress shown multiple influences on chondrocytes, physiologically necessary for maintaining chondrocyte homeostasis and promoting cartilage development, pathologically help for cartilage destruction and OA development via boosting chondrocyte differentiation and hypertrophy and accelerating cell apoptosis.

scholarly journals Network Pharmacology Identifies the Mechanisms of Sang-Xing-Zhi-Ke-Fang against Pharyngitis

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Yinhe Deng ◽  
Quanjiang Li ◽  
Menglin Li ◽  
Tiantian Han ◽  
Guixian Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Influenza A ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Venn Diagram ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Ras Signaling ◽  
Clinical Effects ◽  
Overlapping Genes

Background. Sang-Xing-Zhi-Ke-Fang (SXZKF) demonstrates good therapeutic effect against pharyngitis. Nevertheless, the pharmacological mechanism underlying its effectiveness is still unclear. Objective. To investigate the underlying mechanisms of SXZKF against pharyngitis using network pharmacology method. Methods. Bioactive ingredients of SXZKF were collected and screened using published literature and two public databases. Using four public databases, the overlapping genes between these bioactive compound-related and pharyngitis-related genes were identified by Venn diagram. Protein-protein interaction (PPI) was obtained using “Search Tool for the Retrieval of Interacting Genes (STRING)” database. “Database for Annotation, Visualization, and Integrated Discovery ver. 6.8 (DAVID 6.8)” was used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to explore the molecular mechanisms of SXZKF against pharyngitis. Finally, Cytoscape 3.7.2 software was used to construct and visualize the networks. Result. A total of 102 bioactive compounds were identified. Among them, 886 compounds-related and 6258 pharyngitis-related genes were identified, including 387 overlapping genes. Sixty-three core targets were obtained, including ALB, PPARγ, MAPK3, EGF, and PTGS2. Signaling pathways closely related to mechanisms of SXZKF for pharyngitis were identified, including serotonergic synapse, VEGF signaling pathway, Fc epsilon RI signaling pathway, Ras signaling pathway, MAPK signaling pathway, and influenza A. Conclusion. This is the first identification of in-depth study of SXZKF against pharyngitis using network pharmacology. This new evidence could be informative in providing new support on the clinical effects of SXZKF on pharyngitis and for the development of personalized medicine for pharyngitis.

scholarly journals Comparison of MicroRNA Transcriptomes Reveals the Association between MiR-148a-3p Expression and Rumen Development in Goats

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1951
Author(s):  
Tao Zhong ◽  
Cheng Wang ◽  
Jiangtao Hu ◽  
Xiaoyong Chen ◽  
Lili Niu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Target Genes ◽  
Genetic Regulation ◽  
Mapk Signaling ◽  
Regulation Mechanism ◽  
Ras Signaling ◽  
Genome Wide ◽  
A Genome ◽  
Rumen Development ◽  
And Function

The rumen is an important digestive organ of ruminants. From the fetal to adult stage, the morphology, structure and function of the rumen change significantly. However, the knowledge of the intrinsic genetic regulation of these changes is still limited. We previously reported a genome-wide expression profile of miRNAs in pre-natal goat rumens. In this study, we combined and analyzed the transcriptomes of rumen miRNAs during pre-natal (E60 and E135) and post-natal (D30 and D150) stages. A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the pre-weaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites of miR-148a-3p in the 3′-UTR of QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI through in situ hybridization was observed in the rumen tissues but not in the intestinal tracts. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers of the rumen, suggesting that miR-148a-3p is involved in the development of the rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells. Taken together, our study identified DEMs involved in the development of the rumen and provides insights into the regulation mechanism of rumen development in goats.

Effects of strain and body weight on low-oxygen tolerance of channel catfish (Ictalurus punctatus)

2017 ◽  
Vol 25 (4) ◽  
pp. 1645-1652 ◽  
Author(s):  
Xiaozhu Wang ◽  
Shikai Liu ◽  
Rex Dunham ◽  
Zhanjiang Liu
Keyword(s):  
Body Weight ◽  
Ictalurus Punctatus ◽  
Channel Catfish ◽  
Low Oxygen ◽  
Oxygen Tolerance

Mini review: The FDA-approved prescription drugs that target the MAPK signaling pathway in women with breast cancer

2021 ◽  
pp. 1-12
Author(s):  
Fatemeh Khojasteh Poor ◽  
Mona Keivan ◽  
Mohammad Ramazii ◽  
Farhoodeh Ghaedrahmati ◽  
\unskip\break Amir Anbiyaiee ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Signaling Pathway ◽  
Prescription Drugs ◽  
Mapk Pathway ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Ras Signaling ◽  
Farnesyltransferase Inhibitors ◽  
Metastatic Progression ◽  
Dense Breast Tissue

Breast cancer (BC) is the most common cancer and the prevalent type of malignancy among women. Multiple risk factors, including genetic changes, biological age, dense breast tissue, and obesity are associated with BC. The mitogen-activated protein kinases (MAPK) signaling pathway has a pivotal role in regulating biological functions such as cell proliferation, differentiation, apoptosis, and survival. It has become evident that the MAPK pathway is associated with tumorigenesis and may promote breast cancer development. The MAPK/RAS/RAF cascade is closely associated with breast cancer. RAS signaling can enhance BC cell growth and progression. B-Raf is an important kinase and a potent RAF isoform involved in breast tumor initiation and differentiation. Depending on the reasons for cancer, there are different strategies for treatment of women with BC. Till now, several FDA-approved treatments have been investigated that inhibit the MAPK pathway and reduce metastatic progression in breast cancer. The most common breast cancer drugs that regulate or inhibit the MAPK pathway may include Farnesyltransferase inhibitors (FTIs), Sorafenib, Vemurafenib, PLX8394, Dabrafenib, Ulixertinib, Simvastatin, Alisertib, and Teriflunomide. In this review, we will discuss the roles of the MAPK/RAS/RAF/MEK/ERK pathway in BC and summarize the FDA-approved prescription drugs that target the MAPK signaling pathway in women with BC.

scholarly journals Bioinformatics and Multi-omics Approach to Identify Comorbidities with Application in Schizophrenia with Psychiatric Disorders

2021 ◽  
pp. 35-47
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Protein Interactions ◽  
Depressive Disorders ◽  
Expression Patterns ◽  
Mapk Signaling ◽  
Protein Protein Interactions ◽  
Obsessive Compulsive ◽  
Psychiatric Comorbidities ◽  
Compulsive Disorder

Schizophrenia (SCZ) is a major psychiatric disorder and often presents with psychiatric comorbidities. But, the interactions or links between the pathogenesis of SCZ and comorbidities are not known. In this study, we aimed to develop an integrated multi-omics approach based on gene expression, gene ontology, pathways, protein-protein interactions data that help clinical researchers to assess the links between SCZ and major psychiatric pathologies. We compared the transcriptomic alterations between diseases and controls and observed significant perturbed gene expression patterns i.e. differentially expressed (DEGs) shared among SCZ and major depressive disorders, obsessive-compulsive disorder, alcoholism, eating disorder. We observed deregulated expression of three DEGs, namely, HAPLN1, CNDP1, SLC12A2 in SCZ and pathologies, which were common among the selected pathologies suggesting the selected disorders are comorbidities of SCZ. The pathways including FoxO signaling pathway, MAPK signaling pathway, transcriptional misregulation in cancer, cellular senescence, cell cycle, PI3-Akt signaling pathway, TNF signaling pathway, and TGF-beta signaling pathway altered by the shared SCZ and psychiatric comorbidities also identified. The present study revealed biomolecules (DEGs), ontologies, and cellular pathways of the etiopathogenetic mechanisms of SCZ and psychiatric comorbidities.

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