scholarly journals Elucidating the Molecular Mechanisms by which Seed-Borne Endophytic Fungi, Epichloë gansuensis, Increases the Tolerance of Achnatherum inebrians to NaCl Stress

2021 ◽  
Vol 22 (24) ◽  
pp. 13191
Author(s):  
Chen Cheng ◽  
Jianfeng Wang ◽  
Wenpeng Hou ◽  
Kamran Malik ◽  
Chengzhou Zhao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Molecular Mechanisms ◽  
Ion Homeostasis ◽  
Nacl Stress ◽  
Full Length ◽  
Differentially Expressed ◽  
Achnatherum Inebrians ◽  
Oxidation Reduction ◽  
Dependent Protein ◽  
Simple Sequence

Seed-borne endophyte Epichloë gansuensis enhance NaCl tolerance in Achnatherum inebrians and increase its biomass. However, the molecular mechanism by which E. gansuensis increases the tolerance of host grasses to NaCl stress is unclear. Hence, we firstly explored the full-length transcriptome information of A. inebrians by PacBio RS II. In this work, we obtained 738,588 full-length non-chimeric reads, 36,105 transcript sequences and 27,202 complete CDSs from A. inebrians. We identified 3558 transcription factors (TFs), 15,945 simple sequence repeats and 963 long non-coding RNAs of A. inebrians. The present results show that 2464 and 1817 genes were differentially expressed by E. gansuensis in the leaves of E+ and E− plants at 0 mM and 200 mM NaCl concentrations, respectively. In addition, NaCl stress significantly regulated 4919 DEGs and 502 DEGs in the leaves of E+ and E− plants, respectively. Transcripts associated with photosynthesis, plant hormone signal transduction, amino acids metabolism, flavonoid biosynthetic process and WRKY TFs were differentially expressed by E. gansuensis; importantly, E. gansuensis up-regulated biology processes (brassinosteroid biosynthesis, oxidation–reduction, cellular calcium ion homeostasis, carotene biosynthesis, positive regulation of proteasomal ubiquitin-dependent protein catabolism and proanthocyanidin biosynthesis) of host grass under NaCl stress, which indicated an increase in the ability of host grasses’ adaptation to NaCl stress. In conclusion, our study demonstrates the molecular mechanism for E. gansuensis to increase the tolerance to salt stress in the host, which provides a theoretical basis for the molecular breed to create salt-tolerant forage with endophytes.

scholarly journals Quantitative Proteomics Analysis to Study the Protective Effects of Nerve Growth Factor on Hippocampal Mitochondria in VD Rats

2021 ◽  
Author(s):  
Yanmei Zhang ◽  
yuan yao ◽  
Runxiu Zhu ◽  
Niyang Aida ◽  
Jun Yuan ◽  
...  
Keyword(s):  
Nerve Growth Factor ◽  
Growth Factor ◽  
Molecular Mechanism ◽  
Molecular Mechanisms ◽  
Clinical Syndrome ◽  
Differentially Expressed ◽  
Protective Effects ◽  
Differentially Expressed Proteins ◽  
Sprague Dawley ◽  
Nerve Growth

Abstract Background Vascular dementia (VD) is a kind of clinical syndrome characterized with the impairment cognitive function caused by cerebrovascular disease. Genetics, biochemical, and morphological analyses of cell and animal models, reveal that mitochondria could have roles in this neurodegeneration. Methods We used Sprague-Dawley rats to establish VD model, and used the proteomics method based on relative quantification (iTRAQ) to identify the differentially expressed proteins in hippocampus mitochondria. Results A total of 33 differentially expressed proteins were identified between the VD rats and the VD rats treated with nerve growth factor groups. And five differentially expressed proteins (Rgs14, Slc7a14, Ppm1l, Kcnj10 and Syngr1) were identified after completing the sham-operate control, VD rats and VD rats treated with nerve growth factor groups, then successfully confirmed by western blot. Bioinformatics analysis suggested that the mitochondrial molecular mechanism of VD and the protective effect of nerve growth factor on mitochondrial function of VD rats may be due to different molecular mechanisms. Conclusion We estimated that mitochondrial dysfunction may be the onset of VD and key role in the pathological process of VD. This study not only has a deeper understanding of the mitochondrial molecular mechanism of VD, but also is helpful for the screening of drug targets.

scholarly journals Transcriptome Profiling Provides Insights into Molecular Mechanism in Peanut Semi-dwarf Mutant

2020 ◽  
Author(s):  
Fengdan Guo ◽  
Junjie Ma ◽  
Lei Hou ◽  
Suhua Shi ◽  
Jinbo Sun ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Main Stem ◽  
Differentially Expressed ◽  
Dwarf Mutant ◽  
Mature Stage ◽  
Stem Height

Abstract Background: Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. Results: In this study, a semi-dwarf peanut mutant was identified from 60 Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 ( sdm2 ). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. Conclusions: A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.

scholarly journals A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Nan Deng ◽  
Chen Hou ◽  
Boxiang He ◽  
Fengfeng Ma ◽  
Qingan Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Seed Development ◽  
Molecular Mechanisms ◽  
Immature Stage ◽  
Full Length ◽  
Differentially Expressed ◽  
Mature Stage ◽  
Medicinal Uses ◽  
A Site

Abstract Background Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown. Results We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5726 novel genes, 9061 alternative splicing events, 3551 lncRNAs, 2160 transcription factors, and we found that 8512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7891 genes upregulated and 6432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

scholarly journals Transcriptome Profiling Provides Insights into Molecular Mechanism in Peanut Semi-dwarf Mutant (Arachis hypogaea L.)

2019 ◽  
Author(s):  
Fengdan Guo ◽  
Junjie Ma ◽  
Suhua Shi ◽  
Jinbo Sun ◽  
Guanghui Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Molecular Genetic ◽  
Gene Expression Profiles ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Dwarf Mutant ◽  
Mature Stage ◽  
Causal Genes

Abstract BackgroundPlant height is the major agronomic trait and closely correlated to crop yield. Plant height development is an important area of plant developmental biology and numerous studies about its molecular genetic basis had been conducted on model plants and crops. However, little is known on the molecular mechanisms of peanut plant height.ResultsIn this study, a semi-dwarf peanut mutant was identified from Co60 gama ray induced mutant population and designated as semi-dwarf mutant 2 (sdm2). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. Both the internode number and internode length of sdm2 were less than those of FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The identified differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in both BR biosynthesis and signaling were found to be significantly down-regulated in stem and leaf of sdm2 as compared to FH1. Many transcription factor genes were identified as DEGs.ConclusionsA large number of genes were found to be differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding advanced peanut varieties with semi-dwarf phenotype.

scholarly journals Transcriptome Profiling Provides Insights into Molecular Mechanism in Peanut Semi-dwarf Mutant

2020 ◽  
Author(s):  
Fengdan Guo ◽  
Junjie Ma ◽  
Lei Hou ◽  
Suhua Shi ◽  
Jinbo Sun ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Main Stem ◽  
Differentially Expressed ◽  
Dwarf Mutant ◽  
Mature Stage ◽  
Stem Height

Abstract Background: Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. Results: In this study, a semi-dwarf peanut mutant was identified from 60 Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 ( sdm2 ). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. Conclusions: A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.

scholarly journals Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis

Biomolecules ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 35 ◽  
Author(s):  
Meenashi Vanathi Balashanmugam ◽  
Thippeswamy Boreddy Shivanandappa ◽  
Sivagurunathan Nagarethinam ◽  
Basavaraj Vastrad ◽  
Chanabasayya Vastrad
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Molecular Mechanism ◽  
Differentially Expressed Genes ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Artery Disease

Coronary artery disease (CAD) is a major cause of end-stage cardiac disease. Although profound efforts have been made to illuminate the pathogenesis, the molecular mechanisms of CAD remain to be analyzed. To identify the candidate genes in the advancement of CAD, microarray dataset GSE23766 was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified, and pathway and gene ontology (GO) enrichment analyses were performed. The protein-protein interaction network was constructed and the module analysis was performed using the Biological General Repository for Interaction Datasets (BioGRID) and Cytoscape. Additionally, target genes-miRNA regulatory network and target genes-TF regulatory network were constructed and analyzed. There were 894 DEGs between male human CAD samples and female human CAD samples, including 456 up regulated genes and 438 down regulated genes. Pathway enrichment analyses revealed that DEGs (up and down regulated) were mostly enriched in the superpathway of steroid hormone biosynthesis, ABC transporters, oxidative ethanol degradation III and Complement and coagulation cascades. Similarly, geneontology enrichment analyses revealed that DEGs (up and down regulated) were mostly enriched in the forebrain neuron differentiation, filopodium membrane, platelet degranulation and blood microparticle. In the PPI network and modules (up and down regulated), MYC, NPM1, TRPC7, UBC, FN1, HEMK1, IFT74 and VHL were hub genes. In the target genes-miRNA regulatory network and target genes—TF regulatory network (up and down regulated), TAOK1, KHSRP, HSD17B11 and PAH were target genes. In conclusion, the pathway and GO ontology enriched by DEGs may reveal the molecular mechanism of CAD. Its hub and target genes, MYC, NPM1, TRPC7, UBC, FN1, HEMK1, IFT74, VHL, TAOK1, KHSRP, HSD17B11 and PAH were expected to be new targets for CAD. Our finding provided clues for exploring molecular mechanism and developing new prognostics, diagnostic and therapeutic strategies for CAD.

scholarly journals Screening and evaluation of key genes in contributing to pathogenesis of hepatic fibrosis based on microarray data

2020 ◽  
Vol 25 (1) ◽  
Author(s):  
Furong Wu ◽  
Lijuan Ning ◽  
Ran Zhou ◽  
Aizong Shen
Keyword(s):  
Hepatic Fibrosis ◽  
Molecular Mechanisms ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Protein Protein Interaction ◽  
Functional Studies ◽  
Oxidation Reduction ◽  
Crucial Information ◽  
Underlying Mechanisms

Abstract Background Hepatic fibrosis (HF), which is characterized by the excessive accumulation of extracellular matrix (ECM) in the liver, usually progresses to liver cirrhosis and then death. To screen differentially expressed (DE) long non-coding RNAs (lncRNAs) and mRNAs, explore their potential functions to elucidate the underlying mechanisms of HF. Methods The microarray of GSE80601 was downloaded from the Gene Expression Omnibus database, which is based on the GPL1355 platform. Screening for the differentially expressed LncRNAs and mRNAs was conducted between the control and model groups. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to analyze the biological functions and pathways of the DE mRNAs. Additionally, the protein–protein interaction (PPI) network was delineated. In addition, utilizing the Weighted Gene Co-expression Network Analysis (WGCNA) package and Cytoscape software, we constructed lncRNA-mRNA weighted co-expression networks. Results A total of 254 significantly differentially expressed lncRNAs and 472 mRNAs were identified. GO and KEGG analyses revealed that DE mRNAs regulated HF by participating in the GO terms of metabolic process, inflammatory response, response to wounding and oxidation–reduction. DE mRNAs were also significantly enriched in the pathways of ECM-receptor interaction, PI3K-Akt signaling pathway, focal adhesion (FA), retinol metabolism and metabolic pathways. Moreover, 24 lncRNAs associated with 40 differentially expressed genes were observed in the modules of lncRNA-mRNA weighted co-expression network. Conclusions This study revealed crucial information on the molecular mechanisms of HF and laid a foundation for subsequent genes validation and functional studies, which could contribute to the development of novel diagnostic markers and provide new therapeutic targets for the clinical treatment of HF.

scholarly journals A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

2020 ◽  
Author(s):  
Nan deng ◽  
Chen Hou ◽  
Boxiang He ◽  
Fengfeng Ma ◽  
Qingan Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Seed Development ◽  
Molecular Mechanisms ◽  
Immature Stage ◽  
Full Length ◽  
Differentially Expressed ◽  
Mature Stage ◽  
Medicinal Uses ◽  
A Site

Abstract Background: Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown.Results: We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5,726 novel genes, 9,061 alternative splicing events, 3,551 lncRNAs, 2,160 transcription factors, and we found that 8,512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7,891 genes upregulated and 6,432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense.Conclusions: These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

scholarly journals A Full-length Transcriptome and Gene Expression Analysis Reveal Genes and Molecular Elements Expressed During Seed Development in Gnetum Luofuense

2020 ◽  
Author(s):  
Nan deng ◽  
Chen Hou ◽  
Boxiang He ◽  
Fengfeng Ma ◽  
Qingan Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Expression Analysis ◽  
Molecular Mechanisms ◽  
Immature Stage ◽  
Full Length ◽  
Differentially Expressed ◽  
Mature Stage ◽  
Medicinal Uses ◽  
A Site

Abstract Background: Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and secondary metabolic compounds accumulate during the ripening of Gnetum seeds.However, the molecular mechanisms related to this process remain unknown. Results: We therefore assembled a full-length transcriptome from immature and mature G. luofuenseseeds using PacBio sequencingreads. We identified a total of 5,726 novel genes, 9,061 alternative splicing events, 3,551 lncRNAs, 2,160 transcription factors, and 359 fusion genes, and we found that 8,512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that14,323 genes were differentially expressed from an immature stage to a mature stage with 7,891 genes upregulated and 6,432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions:These findings provide a valuable molecular resource for domestication and cultivation of Gnetum species.

scholarly journals A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

2020 ◽  
Author(s):  
Nan deng ◽  
Chen Hou ◽  
Boxiang He ◽  
Fengfeng Ma ◽  
Qingan Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Seed Development ◽  
Molecular Mechanisms ◽  
Immature Stage ◽  
Full Length ◽  
Differentially Expressed ◽  
Mature Stage ◽  
Medicinal Uses ◽  
A Site

Abstract Background: Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown.Results: We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5,726 novel genes, 9,061 alternative splicing events, 3,551 lncRNAs, 2,160 transcription factors, and we found that 8,512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7,891 genes upregulated and 6,432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense.Conclusions: These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

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