Genes containing GTP_EFTU domain mainly express elongation factors(EF),Small GTPases,and GTP-binding proteins,which are closely related to protein synthesis,extension and ATP synthesis.In this study,we identified 39 g...Genes containing GTP_EFTU domain mainly express elongation factors(EF),Small GTPases,and GTP-binding proteins,which are closely related to protein synthesis,extension and ATP synthesis.In this study,we identified 39 genes containing GTP_EFTU domains from peppers.The evolutionary trees constructed from capsicum,Arabidopsis,rice,and tomato are mainly divided into 7 subfamilies.Using PacBio(Pacific Biosciences)sequencing and assembly data,we extracted these 39 gene sequences,fromwhich 25 genes had alternative splicing.Particularly,the Capana08g000545 had 16 alternative splicing processes.Accordingly,we performed promoter sequence analysis,subcellular location prediction,the expression analysis of different tissues and periods,and also the GO(Gene ontology)analysis of co-expressed genes.Lastly we did the qRTPCR analysis in 5 stages of pepper fruit development.These analyses revealed important structural and functional information for the identified 39 genes that contain GTP_EFTU domains,providing important references for further follow-up experiments to verify the genes function on plants or their unique roles in peppers.展开更多
To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exog...To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened out.The results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other pathways.Carbon metabolism and glutathione metabolism may play an important role in the response of A.blazei mycelium to cadmium stress.展开更多
Objective:To explore the mechanism of Radix Astragali-Lithospermum Erythrorhizon on the treatment of diabetic ulcer through the method of network pharmacology.Methods:This study included 32 compounds and 81 key target...Objective:To explore the mechanism of Radix Astragali-Lithospermum Erythrorhizon on the treatment of diabetic ulcer through the method of network pharmacology.Methods:This study included 32 compounds and 81 key targets.100 GO functional items and 116 KEGG signal pathways were obtained by enrichment analysis.Quercetin,kaempferol,isorhamnetin,mononetin,sitosterol,ivy sapogenin and other components of astragalus-purple herb play a key role in the targets of interleukin-6,cystatin 3,vascular endothelial growth factor,epidermal growth factor receptor and mitogen-activated protein kinase 8 in diabetic ulcer,and are mainly concentrated in AGE-RAGE,TNF and other signal pathways.Results:There were 32 compounds and 81 key targets.100 GO functional items and 116 KEGG signal pathways were obtained by enrichment analysis.Quercetin,kaempferol,isorhamnetin,mononetin,sitosterol,ivy sapogenin and other components of astragalus-purple herb play a key role in the targets of interleukin-6,cystatin 3,vascular endothelial growth factor,epidermal growth factor receptor and mitogen-activated protein kinase 8 in diabetic ulcer,and are mainly concentrated in AGE-RAGE,TNF and other signal pathways.Conclusion:Radix Astragali-Lithospermum Erythrorhizon may play the role of inhibiting inflammation,anti-apoptosis,promoting cell proliferation,angiogenesis and immune regulation through multi-components and multitargets,and play a role in the treatment of diabetic ulcer.展开更多
The global dissemination of H5 avian influenza viruses represents a significant threat to both human and animal health.In thisstudy,we conducted a genome-wide siRNA library screening against the highly pathogenic H5N1 i...The global dissemination of H5 avian influenza viruses represents a significant threat to both human and animal health.In thisstudy,we conducted a genome-wide siRNA library screening against the highly pathogenic H5N1 influenza virus,leading us tothe identification of 457 cellular cofactors(441 proviral factors and 16 antiviral factors)involved in the virus replication cycle.Gene Ontology term enrichment analysis revealed that the candidate gene data sets were enriched in gene categoriesassociated with mRNA splicing via spliceosome in the biological process,integral component of membrane in the cellularcomponent,and protein binding in the molecular function.Reactome pathway analysis showed that the immune system(up to63 genes)was the highest enriched pathway.Subsequent comparisons with four previous siRNA library screenings revealedthat the overlapping rates of the involved pathways were 8.53%-62.61%,which were significantly higher than those of thecommon genes(1.85%-6.24%).Together,our genome-wide siRNA library screening unveiled a panorama of host cellularnetworks engaged in the regulation of highly pathogenic H5N1 influenza virus replication,which may provide potential targetsand strategies for developing novel antiviral countermeasures.展开更多
The FAR1-related sequence(FAR1)gene family consists of transcription factors that originated from transposases and is crucial for light signaling and stress adaptation in plants.Despite the recognized importance of FA...The FAR1-related sequence(FAR1)gene family consists of transcription factors that originated from transposases and is crucial for light signaling and stress adaptation in plants.Despite the recognized importance of FAR1 genes in model organisms,their genomic architecture,structural variability,and expression patterns in Phaseolus vulgaris have yet to be investigated.This study offers the inaugural comprehensive genome-wide identification and characterization of the FAR1 gene family in P.vulgaris.A total of 27 PvulFAR1 genes were identified,and their chromosomal distribution,gene structures,conserved domains,and phylogenetic relationships were analyzed systematically.The promoter regions of these genes were discovered to encompass a diverse range of cis-regulatory elements that respond to light,phytohormones,and abiotic stressors,highlighting their regulatory complexity.In silico expression analysis and quantitative real-time PCR(qRT-PCR)experiments demonstrated differential expression patterns of specific PvulFAR1 genes under salt and drought stress in two commercial bean cultivars.PvulFAR1-10 demonstrated consistent upregulation under both stress conditions,especially in the stress-tolerant cultivar Elkoca-05,indicating its potential role in broad-spectrum stress responsiveness.Gene ontology and protein–protein interaction network analyses revealed that PvulFAR1 proteins are predominantly nuclear-localized transcription factors,enriched in zinc ion binding activity,and associated with transcriptional regulation and nucleobase metabolic processes.The results offer novel perspectives on the evolution,structural complexity,and stress-responsive regulatory functions of the FAR1 gene family in common bean.This fundamental knowledge provides significant candidate genes for additional validation and for developing of genetically improved cultivars with enhanced tolerance to abiotic stresses.Future research should focus on clarifying the downstream targets of essential FAR1 members and their integrative function in plant developmental and stress response networks.展开更多
基金supported by The General Program of National Natural Science Foundation of China(Grant No.C150202)The National Key Research and Development Programof China(Grant No.2019YFD1000300)The Hunan province Key Research and Development Program of China(Grant No.2019NK2191)。
文摘Genes containing GTP_EFTU domain mainly express elongation factors(EF),Small GTPases,and GTP-binding proteins,which are closely related to protein synthesis,extension and ATP synthesis.In this study,we identified 39 genes containing GTP_EFTU domains from peppers.The evolutionary trees constructed from capsicum,Arabidopsis,rice,and tomato are mainly divided into 7 subfamilies.Using PacBio(Pacific Biosciences)sequencing and assembly data,we extracted these 39 gene sequences,fromwhich 25 genes had alternative splicing.Particularly,the Capana08g000545 had 16 alternative splicing processes.Accordingly,we performed promoter sequence analysis,subcellular location prediction,the expression analysis of different tissues and periods,and also the GO(Gene ontology)analysis of co-expressed genes.Lastly we did the qRTPCR analysis in 5 stages of pepper fruit development.These analyses revealed important structural and functional information for the identified 39 genes that contain GTP_EFTU domains,providing important references for further follow-up experiments to verify the genes function on plants or their unique roles in peppers.
文摘To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened out.The results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other pathways.Carbon metabolism and glutathione metabolism may play an important role in the response of A.blazei mycelium to cadmium stress.
基金General project of national natural science foundation of China(No.81774310)Youth project of national natural science foundation of China(No.81804095)。
文摘Objective:To explore the mechanism of Radix Astragali-Lithospermum Erythrorhizon on the treatment of diabetic ulcer through the method of network pharmacology.Methods:This study included 32 compounds and 81 key targets.100 GO functional items and 116 KEGG signal pathways were obtained by enrichment analysis.Quercetin,kaempferol,isorhamnetin,mononetin,sitosterol,ivy sapogenin and other components of astragalus-purple herb play a key role in the targets of interleukin-6,cystatin 3,vascular endothelial growth factor,epidermal growth factor receptor and mitogen-activated protein kinase 8 in diabetic ulcer,and are mainly concentrated in AGE-RAGE,TNF and other signal pathways.Results:There were 32 compounds and 81 key targets.100 GO functional items and 116 KEGG signal pathways were obtained by enrichment analysis.Quercetin,kaempferol,isorhamnetin,mononetin,sitosterol,ivy sapogenin and other components of astragalus-purple herb play a key role in the targets of interleukin-6,cystatin 3,vascular endothelial growth factor,epidermal growth factor receptor and mitogen-activated protein kinase 8 in diabetic ulcer,and are mainly concentrated in AGE-RAGE,TNF and other signal pathways.Conclusion:Radix Astragali-Lithospermum Erythrorhizon may play the role of inhibiting inflammation,anti-apoptosis,promoting cell proliferation,angiogenesis and immune regulation through multi-components and multitargets,and play a role in the treatment of diabetic ulcer.
基金supported by the National Key Research and DevelopmentProgram of China(2021YFD1800203 and 2021YFD1800204)the National Natural Science Foundation of China(NSFC)(32192453,32272979,and 32172847)+2 种基金the China PostdoctoralScience Foundation(2019M660897)the Innovation Program ofChinese Academy of Agricultural Sciences(CAAS-CSLPDCP-202401)the Earmarked Fund for China Agriculture Re-search System(CARS-41-G12)。
文摘The global dissemination of H5 avian influenza viruses represents a significant threat to both human and animal health.In thisstudy,we conducted a genome-wide siRNA library screening against the highly pathogenic H5N1 influenza virus,leading us tothe identification of 457 cellular cofactors(441 proviral factors and 16 antiviral factors)involved in the virus replication cycle.Gene Ontology term enrichment analysis revealed that the candidate gene data sets were enriched in gene categoriesassociated with mRNA splicing via spliceosome in the biological process,integral component of membrane in the cellularcomponent,and protein binding in the molecular function.Reactome pathway analysis showed that the immune system(up to63 genes)was the highest enriched pathway.Subsequent comparisons with four previous siRNA library screenings revealedthat the overlapping rates of the involved pathways were 8.53%-62.61%,which were significantly higher than those of thecommon genes(1.85%-6.24%).Together,our genome-wide siRNA library screening unveiled a panorama of host cellularnetworks engaged in the regulation of highly pathogenic H5N1 influenza virus replication,which may provide potential targetsand strategies for developing novel antiviral countermeasures.
文摘The FAR1-related sequence(FAR1)gene family consists of transcription factors that originated from transposases and is crucial for light signaling and stress adaptation in plants.Despite the recognized importance of FAR1 genes in model organisms,their genomic architecture,structural variability,and expression patterns in Phaseolus vulgaris have yet to be investigated.This study offers the inaugural comprehensive genome-wide identification and characterization of the FAR1 gene family in P.vulgaris.A total of 27 PvulFAR1 genes were identified,and their chromosomal distribution,gene structures,conserved domains,and phylogenetic relationships were analyzed systematically.The promoter regions of these genes were discovered to encompass a diverse range of cis-regulatory elements that respond to light,phytohormones,and abiotic stressors,highlighting their regulatory complexity.In silico expression analysis and quantitative real-time PCR(qRT-PCR)experiments demonstrated differential expression patterns of specific PvulFAR1 genes under salt and drought stress in two commercial bean cultivars.PvulFAR1-10 demonstrated consistent upregulation under both stress conditions,especially in the stress-tolerant cultivar Elkoca-05,indicating its potential role in broad-spectrum stress responsiveness.Gene ontology and protein–protein interaction network analyses revealed that PvulFAR1 proteins are predominantly nuclear-localized transcription factors,enriched in zinc ion binding activity,and associated with transcriptional regulation and nucleobase metabolic processes.The results offer novel perspectives on the evolution,structural complexity,and stress-responsive regulatory functions of the FAR1 gene family in common bean.This fundamental knowledge provides significant candidate genes for additional validation and for developing of genetically improved cultivars with enhanced tolerance to abiotic stresses.Future research should focus on clarifying the downstream targets of essential FAR1 members and their integrative function in plant developmental and stress response networks.
