Functional Annotation of Transcripts Obtained from Fall-Grown Tall Fescue as Influenced by Endophyte Infection

Abstract Tall fescue is one of the primary source of forage for livestock. It grows well in the marginal soils of the temperate zones. It hosts a fungal endophyte (Epichloë coenophiala), which helps the plants to tolerate abiotic and biotic stresses. The genetics and biology underlying mechanism of freezing stress tolerance of tall fescue is still unknown, due to its complex genetic background and outbreeding modes of pollination, limited genomic, and transcriptomic resources. The aim of this study was to identify differentially expressed genes (DEGs) in two tissues between novel endophyte-positive (E+) and endophyte-free (E-) tall fescue genotypes at three diurnal time points; in the morning (-3.0 to 0.5°C), afternoon (11 to 12°C), and evening (12 − 10°C) in the field environment, by exploring the transcriptional landscape via RNA sequencing. For the first time, we generated 226,054 and 224,376 transcripts from E + and E- Texoma MaxQ II tall fescue, respectively by de novo assembly. The upregulated transcripts were detected fewer than the downregulated ones in both tissues (S: 803 up and 878 down; L: 783 up and 846 down) under the freezing temperatures in the morning. By Gene Ontology enrichment analysis, 10 GO terms were found only under the freezing stress in the morning. Metabolic pathway and biosynthesis of secondary metabolites genes showed lowest number of DEGs under morning freezing stress and highest number in evening cold condition by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. The DEGs expressed under morning stress condition and the nine candidate genes that we identified using GO analysis, might be the possible route underlying cold tolerance in tall fescue.

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Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Genes ◽

10.3390/genes11060631 ◽

2020 ◽

Vol 11 (6) ◽

pp. 631

Author(s):

Zhicheng Sun ◽

Fangrui Lou ◽

Yuan Zhang ◽

Na Song

Keyword(s):

Signal Transduction ◽

Salinity Stress ◽

De Novo ◽

Enrichment Analysis ◽

Gill Tissue ◽

Control Group ◽

Rna Seq ◽

Illumina Hiseq ◽

Kegg Pathways ◽

Pathways Analysis

Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.

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Bioinformatic Analysis: Screening and Identification of Differentially Expressed Genes Modified by m6A in Ovarian Cancer

10.21203/rs.3.rs-111366/v1 ◽

2020 ◽

Author(s):

Huidong Liu ◽

Wen-wen Zhang ◽

Ge Lou

Keyword(s):

Ovarian Cancer ◽

Differentially Expressed Genes ◽

Clinical Sample ◽

Therapeutic Targets ◽

Enrichment Analysis ◽

Underlying Mechanism ◽

Bioinformatic Analysis ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Kegg Pathways

Abstract Background: N6-methyladenosine(m6A) is one of the most common RNA modifications that occurs at the nitrogen-6 position of adenine. Emerging evidence has revealed that regulatory functions of m6A play an essential role in the development of cancer. However the study of m6A in ovarian cancer(OC) is still in our infancy. In this work ,we aimed to identify and analysis the differentially expressed genes(DEGs） modified by m6A which can provide new therapeutic targets and key biomarkers in OC.Methods: We downloaded Microarray datasets GSE146553 and GSE124766 from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by GEO2R analysis tools. Subsequently, The DAVID database was used to construct Enrichment analysis of GO and KEGG pathways. Next, the DEGs modified by m6A were identified by m6AVar database. Finally, the functional analysis and clinical sample validation of these genes were verified by ONCOMINE, GEPIA, cBioPortal online platform and Kaplan-Meier Plotter.Results:152 DEGs were selected ,and the DEGs were mainly enriched in extracellular exosome, spindle microtubule, response to hypoxia and cell cycle .And we identified 15 DEGs which were modified by m6A:MAPK10、MXRA5、CHD7、MECOM、SCN7A、GREB、PRUNE2、MX2、TOP2A、JAM2、DST、LAPTM5、CDKN2A、GATM and ANGPTL1. After statistical analysis, two DEGs (SCN7A and GAMT) were selected for detailed study. We revealed that SCN7A and GAMT were expressed at a low level in OC. Afterwards, Survival analysis showed that SCN7A and GAMT expression were correlated with OC overall survival. And the expression of SCN7A and GAMT mRNA decreasing in different TNM stages. Finally, we presumed that the modification of m6A spongs GAMT via EIF4A3 or FUS to participate in the occcurrence and the development of OC.Conclusion: Altogether, the current study identified and analysised the DEGs modified by m6A in OC. It will help us to investigate the underlying mechanism and progression of OC. In addition, it can provide new diagnostic markers and potential therapeutic targets in OC.

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RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

Scientific Reports ◽

10.1038/s41598-020-76234-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Himansu Kumar ◽

Hyojun Choo ◽

Asankadyr U. Iskender ◽

Krishnamoorthy Srikanth ◽

Hana Kim ◽

...

Keyword(s):

Enrichment Analysis ◽

Mapk Signaling ◽

Climatic Conditions ◽

Rna Seq ◽

Kegg Pathways ◽

Go Enrichment ◽

Commercial Chicken ◽

Pathways Analysis ◽

Ppar Signaling ◽

Transcriptome Expression

Abstract Transcriptome expression reflects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profile multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as differentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were differentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT-PCR result also corroborated the RNA-Seq findings with R2 of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our findings can improve the understanding of environmental acclimation process in chicken.

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Deciphering the Underlying Mechanism of Eucommiae Cortex against Osteoporotic Fracture by Network Pharmacology

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/7049812 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Yongming Shuai ◽

Zhili Jiang ◽

Qiuwen Yuan ◽

Shuqiang Tu ◽

Fanhui Zeng

Keyword(s):

Osteoporotic Fractures ◽

Enrichment Analysis ◽

Underlying Mechanism ◽

Ovariectomized Rats ◽

Network Pharmacology ◽

Future Research ◽

Ppi Network ◽

Hub Genes ◽

Traditional Chinese Herbal Medicine ◽

Kegg Pathways

Background. Du Zhong (DZ), or Eucommiae Cortex, a traditional Chinese herbal medicine, has been used to treat osteoporosis. Although it has been reported that DZ can improve bone mass in ovariectomized rats, its pharmacological mechanisms in treating osteoporotic fractures (OPF) remain unclear. Methods. In this study, we used a network pharmacological manner to explore its potential complicated mechanism in treating OPF. We obtained DZ compounds from TCMSP and BATMAN-TCM databases and collected potential targets of these compounds through target fishing based on TCMSP and BATMAN-TCM databases. Next, we collected the OPF targets by using CTD, GeneCards, OMIM, HPO, and GenCLiP 3 databases. And then the overlapping genes between DZ potential targets and OPF targets were used to build up the protein-protein interaction (PPI) network and to analyze their interactions and find out the big hub genes in this network. Subsequently, clusterProfiler package in R language was utilized to conduct the enrichment of Gene Ontology biological process and KEGG pathways. Results. There were totally 93 active compounds and 916 related targets in DZ. After the enrichment analysis, we collected top 25 cellular biological processes and top 25 pathways based on the adjusted P value and found that the DZ anti-OPF effect was mainly associated with the regulation of ROS and inflammatory response. Furthermore, 64 hub genes in PPI network, such as MAPK1 (degree = 41), SRC (degree = 39), PIK3R1 (degree = 36), VEGFA (degree = 31), TP53 (degree = 29), EGFR (degree = 29), JUN (degree = 29), AGT (degree = 29), MAPK1, SRC, PIK3R1, VEGFA, and TP53, were considered as potential therapeutic targets, implying the underlying mechanisms of DZ acting on OPF. Conclusion. We investigated the possible therapeutic mechanisms of DZ from a systemic perspective. These key targets and pathways provided promising directions for the future research to reveal the exact regulating mechanisms of DZ in treating OPF.

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Bufalin: A Systematic Review of Research Hotspots and Antitumor Mechanisms by Text Mining and Bioinformatics

The American Journal of Chinese Medicine ◽

10.1142/s0192415x20500810 ◽

2020 ◽

Vol 48 (07) ◽

pp. 1633-1650

Author(s):

Xian Zhang ◽

Xiaoxuan Zhao ◽

Kaili Liu ◽

Yuxuan Che ◽

Xun Qiu ◽

...

Keyword(s):

Network Analysis ◽

Signaling Pathway ◽

Enrichment Analysis ◽

Ppi Network ◽

Protein Protein Interaction ◽

Kegg Pathways ◽

Mesh Terms ◽

Go Enrichment ◽

Pubmed Database ◽

Pathways Analysis

Bufalin is an anticancer drug extract from traditional Chinese medicine. Several articles about bufalin have been published. However, the literature on bufalin has not yet been systematically studied. This study aimed to identify the study status and knowledge structures of bufalin and to summarize the antitumor mechanism. Data were retrieved and downloaded from the PubMed database. The softwares of BICOMB, gCLUTO, Ucinet 6.0, and NetDraw2.084 were used to analyze these publications. The bufalin related genes were recognized and tagged by ABNER software. Then these BF-related genes were performed by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, and protein-protein interaction (PPI) network analysis. A total of 474 papers met the search criteria from 2000 to 2019. By biclustering clustering analysis, the 50 high-frequency main MeSH terms/subheadings were classified into 5 clusters. The clusters of drug therapy and the mechanism of bufalin were hotspot topics. A total of 50 genes were identified as BF-related genes. PPI network analysis showed that inducing apoptosis was the main effect of bufalin, and apoptosis-related gene Caspase 3 was the most reported by people. Bufalin could inhibit the proliferation, invasion, and metastasis of cancer cells through multiple signaling pathways, such as PI3K/AKT, Hedgehog, MAPK/JNK, Wnt/[Formula: see text]-catenin, TGF-[Formula: see text]/Smad, Integrin signaling pathway, and NF-KB signaling pathway via KEGG analysis. Through the quantitative analysis of bufalin literature, we revealed the research status and hot spots in this field and provided some guidance for further research.

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Fatherhood alters gene expression within the MPOA

10.1101/258111 ◽

2018 ◽

Author(s):

Adele M. H. Seelke ◽

Jessica M. Bond ◽

Trent C. Simmons ◽

Nikhil Joshi ◽

Matthew L. Settles ◽

...

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Paternal Care ◽

Mammalian Species ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Prairie Voles ◽

Kegg Pathways ◽

Pathways Analysis ◽

New Gene

AbstractFemale parenting is obligate in mammals, but fathering behavior among mammals is rare. Only 3–5% of mammalian species exhibit biparental care, including humans, and mechanisms of fathering behavior remain sparsely studied. However, in species where it does exist, paternal care is often crucial to the survivorship of offspring. The present study is the first to identify new gene targets linked to the experience of fathering behavior in a biparental species using RNA sequencing. In order to determine the pattern of gene expression within the medial preoptic area that is specifically associated with fathering behavior, we identified differentially expressed genes in male prairie voles (Microtus ochrogaster) that experienced one of three social conditions: virgin males, pair bonded males, and males with fathering experience. Differentially expressed genes from each comparison (i.e., Virgin vs Paired, Virgin vs Fathers, and Paired vs Fathers) were evaluated using the Gene Ontology enrichment analysis, and Kegg pathways analysis to reveal metabolic pathways associated with specific differentially expressed genes. Using these tools, we identified a group of genes that are differentially expressed in voles with different amounts of social experience. These genes are involved in a variety of processes, with particular enrichment in genes associated with immune function, metabolism, synaptic plasticity, and the remodeling of dendritic spines. The identification of these genes and processes will lead to novel insights into the biological basis of fathering behavior.

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Cancer-associated fibroblasts promote the survival of irradiated nasopharyngeal carcinoma cells via the NF-κB pathway

Journal of Experimental & Clinical Cancer Research ◽

10.1186/s13046-021-01878-x ◽

2021 ◽

Vol 40 (1) ◽

Cited By ~ 1

Author(s):

Weiqiang Huang ◽

Longshan Zhang ◽

Mi Yang ◽

Xixi Wu ◽

Xiaoqing Wang ◽

...

Keyword(s):

Dna Damage ◽

Nasopharyngeal Carcinoma ◽

Enrichment Analysis ◽

Underlying Mechanism ◽

Gene Set Enrichment Analysis ◽

Cancer Associated Fibroblasts ◽

Western Blot Assay ◽

Damage Level ◽

Radiation Resistant

Abstract Background Irradiation has emerged as a valid tool for nasopharyngeal carcinoma (NPC) in situ treatment; however, NPC derived from tissues treated with irradiation is a main cause cancer-related death. The purpose of this study is to uncover the underlying mechanism regarding tumor growth after irradiation and provided potential therapeutic strategy. Methods Fibroblasts were extracted from fresh NPC tissue and normal nasopharyngeal mucosa. Immunohistochemistry was conducted to measure the expression of α-SMA and FAP. Cytokines were detected by protein array chip and identified by real-time PCR. CCK-8 assay was used to detect cell proliferation. Radiation-resistant (IRR) 5-8F cell line was established and colony assay was performed to evaluate tumor cell growth after irradiation. Signaling pathways were acquired via gene set enrichment analysis (GSEA). Comet assay and γ-H2AX foci assay were used to measure DNA damage level. Protein expression was detected by western blot assay. In vivo experiment was performed subcutaneously. Results We found that radiation-resistant NPC tissues were constantly infiltrated with a greater number of cancer-associated fibroblasts (CAFs) compared to radiosensitive NPC tissues. Further research revealed that CAFs induced the formation of radioresistance and promoted NPC cell survival following irradiation via the IL-8/NF-κB pathway to reduce irradiation-induced DNA damage. Treatment with Tranilast, a CAF inhibitor, restricted the survival of CAF-induced NPC cells and attenuated the of radioresistance properties. Conclusions Together, these data demonstrate that CAFs can promote the survival of irradiated NPC cells via the NF-κB pathway and induce radioresistance that can be interrupted by Tranilast, suggesting the potential value of Tranilast in sensitizing NPC cells to irradiation.

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Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain

Neuroinformatics ◽

10.1007/s12021-021-09511-0 ◽

2021 ◽

Author(s):

Nestor Timonidis ◽

Alberto Llera ◽

Paul H. E. Tiesinga

Keyword(s):

Gene Expression ◽

Mouse Brain ◽

Structural Connectivity ◽

Enrichment Analysis ◽

Underlying Mechanism ◽

Synaptic Function ◽

Reticular Nucleus ◽

Sources Of Information ◽

Independent Components ◽

Brain Connectome

AbstractFinding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.

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Cellular factors important for the de novo formation of yeast prions

Biochemical Society Transactions ◽

10.1042/bst0361083 ◽

2008 ◽

Vol 36 (5) ◽

pp. 1083-1087 ◽

Cited By ~ 11

Author(s):

Mick Tuite ◽

Klement Stojanovski ◽

Frederique Ness ◽

Gloria Merritt ◽

Nadejda Koloteva-Levine

Keyword(s):

De Novo ◽

Prion Diseases ◽

Underlying Mechanism ◽

Structural Form ◽

Yeast Saccharomyces Cerevisiae ◽

Yeast Prions ◽

Cellular Factors ◽

Jakob Disease ◽

Protein Rich ◽

Cis And Trans

Prions represent an unusual structural form of a protein that is ‘infectious’. In mammals, prions are associated with fatal neurodegenerative diseases such as CJD (Creutzfeldt–Jakob disease), while in fungi they act as novel epigenetic regulators of phenotype. Even though most of the human prion diseases arise spontaneously, we still know remarkably little about how infectious prions form de novo. The [PSI+] prion of the yeast Saccharomyces cerevisiae provides a highly tractable model in which to explore the underlying mechanism of de novo prion formation, in particular identifying key cis- and trans-acting factors. Most significantly, the de novo formation of [PSI+] requires the presence of a second prion called [PIN+], which is typically the prion form of Rnq1p, a protein rich in glutamine and aspartic acid residues. The molecular mechanism by which the [PIN+] prion facilitates de novo [PSI+] formation is not fully established, but most probably involves some form of cross-seeding. A number of other cellular factors, in particular chaperones of the Hsp70 (heat-shock protein 70) family, are known to modify the frequency of de novo prion formation in yeast.

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Bioinformatics analysis of differentially expressed genes and pathways in the development of cervical cancer

BMC Cancer ◽

10.1186/s12885-021-08412-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Baojie Wu ◽

Shuyi Xi

Keyword(s):

Gene Expression ◽

Cervical Cancer ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Molecular Targets ◽

Enrichment Analysis ◽

Ppi Network ◽

Hub Genes ◽

Kegg Pathways

Abstract Background This study aimed to explore and identify key genes and signaling pathways that contribute to the progression of cervical cancer to improve prognosis. Methods Three gene expression profiles (GSE63514, GSE64217 and GSE138080) were screened and downloaded from the Gene Expression Omnibus database (GEO). Differentially expressed genes (DEGs) were screened using the GEO2R and Venn diagram tools. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Gene set enrichment analysis (GSEA) was performed to analyze the three gene expression profiles. Moreover, a protein–protein interaction (PPI) network of the DEGs was constructed, and functional enrichment analysis was performed. On this basis, hub genes from critical PPI subnetworks were explored with Cytoscape software. The expression of these genes in tumors was verified, and survival analysis of potential prognostic genes from critical subnetworks was conducted. Functional annotation, multiple gene comparison and dimensionality reduction in candidate genes indicated the clinical significance of potential targets. Results A total of 476 DEGs were screened: 253 upregulated genes and 223 downregulated genes. DEGs were enriched in 22 biological processes, 16 cellular components and 9 molecular functions in precancerous lesions and cervical cancer. DEGs were mainly enriched in 10 KEGG pathways. Through intersection analysis and data mining, 3 key KEGG pathways and related core genes were revealed by GSEA. Moreover, a PPI network of 476 DEGs was constructed, hub genes from 12 critical subnetworks were explored, and a total of 14 potential molecular targets were obtained. Conclusions These findings promote the understanding of the molecular mechanism of and clinically related molecular targets for cervical cancer.

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