Transferrin receptor 1(TfR1),encoded by the TFRC gene,is the gatekeeper of cellular iron uptake for cells.A variety of molecular mechanisms are at work to tightly regulate TfR1 expression,and abnormal TfR1 expression ...Transferrin receptor 1(TfR1),encoded by the TFRC gene,is the gatekeeper of cellular iron uptake for cells.A variety of molecular mechanisms are at work to tightly regulate TfR1 expression,and abnormal TfR1 expression has been associated with various diseases.In the current study,to determine the regulation pattern of TfR1,we cloned and overexpressed the human TFRC gene in HeLa cells.RNA-sequencing(RNA-seq)was used to analyze the global transcript levels in overexpressed(OE)and normal control(NC)samples.A total of 1669 differentially expressed genes(DEGs)were identified between OE and NC.Gene ontology(GO)analysis was carried out to explore the functions of the DEGs.It was found that multiple DEGs were associated with ion transport and immunity.Moreover,the regulatory network was constructed on basis of DEGs associated with ion transport and immunity,highlighting that TFRC was the node gene of the network.These results together suggested that precisely controlled TfR1 expression might be not only essential for iron homeostasis,but also globally important for cell physiology,including ion transport and immunity.展开更多
[ Objective] In order to study the susceptibility molecular mechanism of highly pathogenic porcine reproductive and respiratory syndrome virus （ HP- PRRSV） JXA1 isolate on Tibetan pig, Zangmei pig and Yorkshire pig....[ Objective] In order to study the susceptibility molecular mechanism of highly pathogenic porcine reproductive and respiratory syndrome virus （ HP- PRRSV） JXA1 isolate on Tibetan pig, Zangmei pig and Yorkshire pig. [ Method ] In the study, real-time quantitative RT-PCR method was established to compare and analyze the differential expression of five porcine reproductive and respiratory syndrome virus （PRRSV） receptor genes （HSPG2, SIGLEC1, CD163, VIM and NMMHC-H A） in lung tissues in Tibetan pig, Zangmei pig and Yorkshire pig before the challenge and at the 4th ,7th and 14th days after the challenge with JXAI isolate. [ Results ] HSPG2 expression in Tibetan pig lung tissues increased significantly at the 4th and 14th days after the challenge with JXAI （ P 〈 0.05 ）, while decreased significantly at the 7th day after the challenge （P 〈 0.05 ）, HSPG2 expression in Zangmei pig lung tissues increased significantly at the 14th day after the challenge （P〈0.05）. SIGLECl expression in Tibetan pig lung tissues increased significantly at the 4th and 14th days after the infection（P 〈 0.05 ）, while SIGLEC 1 expression in Yorkshire pig decreased significantly at the 4th, 7th and 14th days after the challenge （P 〈0. 05 ）. CD163 expression in lung tissues of Tibetan pig and Zangmei pig both increased significantly at the 14th day after the challenge （P 〈 0.05 ）, while CD163 expression in lung tissues of Yorkshire pig decreased significantly at the 7th and 14th days after the challenge （ P 〈 0. 05 ）. VIM expression in lung tissues of Tibetan pig increased significantly at the 7th day after the challenge （ P 〈 0. 05 ）, while which of Yorkshire pig at the 7th day after the challenge decreased significantly （ P 〈 0. 05 ）. NMMHC-II A expression in lung tissues of Zangmei pig increased significantly at the 4th day after the challenge （ P 〈 0. 05 ）, and which of Yorkshire pig increased significantly at the 4th and 14th days after the challenge （P 〈 0. 05 ）. [ Conclusion] SIGLEC1 and VIM genes might be the potential key genes affecting the susceptibility of JXA1 isolate on Tibetan pig, Zangrnei pig and Yorkshire pig. Key words JXA1 isolate; Tibetan pig; Zangmei pig; Yorkshire pig; Porcine reproductive and respiratory syndrome virus receptor genes; Differential expression展开更多
Photoperiodic response is an important characteristic that plays an important role in plant adaptability for various environments. Wheat cultivars grow widely and have high yield potential for the strong photoperiod a...Photoperiodic response is an important characteristic that plays an important role in plant adaptability for various environments. Wheat cultivars grow widely and have high yield potential for the strong photoperiod adaptibility. To assess the photoperiodic response of different genotypes in wheat cultivars, the photoperiodic effects of the Ppd-D1 alleles and the expressions of the related TaGI, TaCO and Ta FT genes in Liaochun 10 and Ningchun 36 were investigated under the short-day（6 h light, SD）, moderate-day（12 h light, MD） and long-day（24 h light, LD） conditions. Amplicon length comparison indicated that the promoter of Ppd-D1 in Ningchun 36 is intact, while Liaochun 10 presented the partial sequence deletion of Ppd-D1 promoter. The durations of all developmental stages of the two cultivars were reduced by subjection to an extended photoperiod, except for the stamen and pistil differentiation stage in the Liaochun 10 cultivar. The expression levels of the Ppd-D1 alleles and the TaGI, TaCO and TaFT genes associated with the photoperiod pathway were examined over a 24-h period under SD and MD conditions. The relationships of different photoperiodic responses of the two cultivars and the expression of photoperiod pathway genes were analyzed accordingly. The photoperiod insensitive（PI） genotype plants flower early under SD; meanwhile, the abnormal expression of the Ppd-D1 a allele is accompanied with an increase in Ta FT1 expression and the TaCO expression variation. The results would facilitate molecular breeding in wheat.展开更多
BACKGROUND Colorectal cancer(CRC)is one of the most malignant gastrointestinal cancers worldwide.The liver is the most important metastatic target organ,and liver metastasis is the leading cause of death in patients w...BACKGROUND Colorectal cancer(CRC)is one of the most malignant gastrointestinal cancers worldwide.The liver is the most important metastatic target organ,and liver metastasis is the leading cause of death in patients with CRC.Owing to the lack of sensitive biomarkers and unclear molecular mechanism,the occurrence of liver metastases cannot be predicted and the clinical outcomes are bad for liver metastases.Therefore,it is very important to identify the diagnostic or prognostic markers for liver metastases of CRC.AIM To investigate the highly differentially expressed genes(HDEGs)and prognostic marker for liver metastases of CRC.METHODS Data from three NCBI Gene Expression Omnibus(GEO)datasets were used to show HDEGs between liver metastases of CRC and tumour or normal samples.These significantly HDEGs of the three GEO datasets take the interactions.And these genes were screened through an online tool to explore the prognostic value.Then,TIMER and R package were utilized to investigate the immunity functions of the HDEGs and gene set enrichment analysis was used to explore their potential functions.RESULTS Based on the selection criteria,three CRC datasets for exploration(GSE14297,GSE41258,and GSE49355)were chosen.Venn diagrams were used to show HDEGs common to the six groups and 47 HDEGs were obtained.The HDEGs were shown by using STRING and Cytoscape software.Based on the TCGA database,APOC1 showed significantly different expression between N2 and N0,and N2 and N1.And there was also a significant difference in expression between T2 and T4,and between T2 and T3.In 20 paired CRC and normal tissues,quantitative real-time polymerase chain reaction illustrated that the APOC1 mRNA was strongly upregulated in CRC tissues(P=0.014).PrognoScan and GEPIA2 revealed the prognostic value of APOC1 for overall survival and diseasefree survival in CRC(P<0.05).TIMER showed that APOC1 has a close relationship with immune infiltration(P<0.05).CONCLUSION APOC1 is a biomarker that is associated with both the diagnosis and prognosis of liver metastases of CRC.展开更多
目的:探讨电压门控钾通道亚家族G成员1(potassium voltage-gated channel subfamily G member 1,KCNG1)在人肺癌组织中的表达水平和临床意义以及其在肺癌细胞恶性生物学行为中的作用。方法:通过TCGA数据库(The Cancer Genome Atlas)分析...目的:探讨电压门控钾通道亚家族G成员1(potassium voltage-gated channel subfamily G member 1,KCNG1)在人肺癌组织中的表达水平和临床意义以及其在肺癌细胞恶性生物学行为中的作用。方法:通过TCGA数据库(The Cancer Genome Atlas)分析KCNG1 mRNA在人肺癌组织中的表达水平,探究其与肺癌患者临床病理特征及预后的关系;基于KCNG1 mRNA表达水平构建预测肺癌患者预后的列线图模型;采用基因本体(GO)功能富集分析和京都基因与基因组百科全书通路(KEGG)富集分析探究KCNG1潜在的生物学功能;采用基因集富集分析(GSEA)预测KCNG1相关差异表达基因参与调控的相关信号通路。采用实时荧光定量PCR(qRT-PCR)及蛋白免疫印迹分别检测肺癌A549和H1299细胞系以及正常肺上皮细胞中KCNG1 mRNA和蛋白表达水平;通过转染siRNA构建KCNG1敲减的细胞株,分别采用EdU,Transwell,Matrigel Transwell,细胞划痕愈合及血管生成拟态实验检测细胞株生物学行为变化。结果:KCNG1 mRNA在肺癌组织中显著高表达且与肺癌患者不良预后密切相关(P均<0.05);列线图模型初步证实KCNG1可能是肺癌潜在的生物标志物,并具有良好的预后评价功能;GO及KEGG富集分析提示KCNG1在调节激素分泌、离子转运、神经肽信号通路及细胞间黏附等生物学过程中发挥重要作用;GSEA结果提示KCNG1相关差异表达基因主要富集在KRAS,MTORC1,MYC,P53及WNT信号通路;KCNG1敲低的肺癌细胞增殖、迁移、侵袭和成管能力明显受到抑制(P均<0.05)。结论:KCNG1 mRNA在肺癌中显著高表达且与患者不良预后密切相关;siRNA介导的KCNG1敲低可显著抑制肺癌细胞的恶性生长。展开更多
Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing toler...Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance.This study evaluated four traits(mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12)related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms(SNPs).The genomewide association study detected that 273 SNPs were in linkage disequilibrium(LD)with the genetic basis of maize deep-sowing tolerance.The RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes(DEGs)in two comparisons,which shared 281 DEGs.By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs,we identified seven candidate genes,of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein.GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length,auxin,or light response.Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length.Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines.These results suggest that GRMZM2G119769 is the most likely candidate gene.This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes,which would be useful for further research on maize deep-sowing tolerance.展开更多
[Objectives]This study was conducted to determine the functions of eight ORF genes of porcine circovirus-like virus P1.[Methods]The double-copy tandem molecular cloning of porcine circovirus-like virus P1 genome was u...[Objectives]This study was conducted to determine the functions of eight ORF genes of porcine circovirus-like virus P1.[Methods]The double-copy tandem molecular cloning of porcine circovirus-like virus P1 genome was used to construct molecular clones with eight ORFs deleted by DNA site-directed mutagenesis technology.After transfected into PK15 cells for a certain period of time,RNA were extracted and was used to verify whether the eight ORFs were deleted or not and used for gene microarry analysis.The GO functions and KEGG pathway enrichment of differentially expressed genes were analyzed.[Results]P1 ORF1 is mainly involved in the biological processes of defense response to virus,signal transduction,regulation of Rab GTPase activity,and lipid metabolic process,and involved in the molecular functions of protein phosphatase inhibitor activity,phosphatidylinositol phospholipase C activity,2 iron,2 sulfur cluster binding,phosphoric diester hydrolase activity,and Rab GTPase activator activity,and in the KEGG pathways of secretion of digestive gland and nervous system development.P1 ORF2 is mainly involved in the biological processes of positive regulation of leukocyte chemotaxis,positive regulation of cell proliferation,positive regulation of cell migration,defense response to virus,regulation of cell growth,and involved in the molecular functions of insulin-like growth factor binding,and chemokine activity,and in the KEGG pathways of cytosolic DNA-sensing pathway,RIG-I-like receptor signaling pathway,toll-like receptor signaling pathway,chemokine signaling pathway,and cytokines,cytokine-cytokine receptor interaction.The biological processes,molecular functions and related pathways involving P1 ORF3 and ORF5 are basically similar to those of ORF2.P1 ORF8 is mainly involved in the biological processes of purine ribonucleotide biosynthetic process,amino acid transport,defense response to virus,amino acid transmembrane transport,and involved in molecular functions of N6-(1,2-dicarboxyethyl)AMP AMP-lyase(fumarate-forming)activity,iron-sulfur cluster binding,amino acid transmembrane transporter activity.[Conclusions]The analysis of the ORF functions of P1 virus lays a foundation for the study of its pathogenicity and pathogenesis.展开更多
基金The work was supported by the General Fund of Health Commission of Hubei Province(No.WJ2019M147).
文摘Transferrin receptor 1(TfR1),encoded by the TFRC gene,is the gatekeeper of cellular iron uptake for cells.A variety of molecular mechanisms are at work to tightly regulate TfR1 expression,and abnormal TfR1 expression has been associated with various diseases.In the current study,to determine the regulation pattern of TfR1,we cloned and overexpressed the human TFRC gene in HeLa cells.RNA-sequencing(RNA-seq)was used to analyze the global transcript levels in overexpressed(OE)and normal control(NC)samples.A total of 1669 differentially expressed genes(DEGs)were identified between OE and NC.Gene ontology(GO)analysis was carried out to explore the functions of the DEGs.It was found that multiple DEGs were associated with ion transport and immunity.Moreover,the regulatory network was constructed on basis of DEGs associated with ion transport and immunity,highlighting that TFRC was the node gene of the network.These results together suggested that precisely controlled TfR1 expression might be not only essential for iron homeostasis,but also globally important for cell physiology,including ion transport and immunity.
基金Supported by Sichuan Public Welfare Scientific Research Institutes Basic Research Projects(SASA2015A03)Sichuan Science and Technology Support Program(2014NZ009,16ZC2850)National Pig Industry Technology System(CARS-36)
文摘[ Objective] In order to study the susceptibility molecular mechanism of highly pathogenic porcine reproductive and respiratory syndrome virus （ HP- PRRSV） JXA1 isolate on Tibetan pig, Zangmei pig and Yorkshire pig. [ Method ] In the study, real-time quantitative RT-PCR method was established to compare and analyze the differential expression of five porcine reproductive and respiratory syndrome virus （PRRSV） receptor genes （HSPG2, SIGLEC1, CD163, VIM and NMMHC-H A） in lung tissues in Tibetan pig, Zangmei pig and Yorkshire pig before the challenge and at the 4th ,7th and 14th days after the challenge with JXAI isolate. [ Results ] HSPG2 expression in Tibetan pig lung tissues increased significantly at the 4th and 14th days after the challenge with JXAI （ P 〈 0.05 ）, while decreased significantly at the 7th day after the challenge （P 〈 0.05 ）, HSPG2 expression in Zangmei pig lung tissues increased significantly at the 14th day after the challenge （P〈0.05）. SIGLECl expression in Tibetan pig lung tissues increased significantly at the 4th and 14th days after the infection（P 〈 0.05 ）, while SIGLEC 1 expression in Yorkshire pig decreased significantly at the 4th, 7th and 14th days after the challenge （P 〈0. 05 ）. CD163 expression in lung tissues of Tibetan pig and Zangmei pig both increased significantly at the 14th day after the challenge （P 〈 0.05 ）, while CD163 expression in lung tissues of Yorkshire pig decreased significantly at the 7th and 14th days after the challenge （ P 〈 0. 05 ）. VIM expression in lung tissues of Tibetan pig increased significantly at the 7th day after the challenge （ P 〈 0. 05 ）, while which of Yorkshire pig at the 7th day after the challenge decreased significantly （ P 〈 0. 05 ）. NMMHC-II A expression in lung tissues of Zangmei pig increased significantly at the 4th day after the challenge （ P 〈 0. 05 ）, and which of Yorkshire pig increased significantly at the 4th and 14th days after the challenge （P 〈 0. 05 ）. [ Conclusion] SIGLEC1 and VIM genes might be the potential key genes affecting the susceptibility of JXA1 isolate on Tibetan pig, Zangrnei pig and Yorkshire pig. Key words JXA1 isolate; Tibetan pig; Zangmei pig; Yorkshire pig; Porcine reproductive and respiratory syndrome virus receptor genes; Differential expression
基金supported by the Key Technologies R&D Program of China during the 12th Five-Year Plan period(2011BAD16B07,2013BAD04B01)the National Natural Science Foundation of China(31271726)
文摘Photoperiodic response is an important characteristic that plays an important role in plant adaptability for various environments. Wheat cultivars grow widely and have high yield potential for the strong photoperiod adaptibility. To assess the photoperiodic response of different genotypes in wheat cultivars, the photoperiodic effects of the Ppd-D1 alleles and the expressions of the related TaGI, TaCO and Ta FT genes in Liaochun 10 and Ningchun 36 were investigated under the short-day（6 h light, SD）, moderate-day（12 h light, MD） and long-day（24 h light, LD） conditions. Amplicon length comparison indicated that the promoter of Ppd-D1 in Ningchun 36 is intact, while Liaochun 10 presented the partial sequence deletion of Ppd-D1 promoter. The durations of all developmental stages of the two cultivars were reduced by subjection to an extended photoperiod, except for the stamen and pistil differentiation stage in the Liaochun 10 cultivar. The expression levels of the Ppd-D1 alleles and the TaGI, TaCO and TaFT genes associated with the photoperiod pathway were examined over a 24-h period under SD and MD conditions. The relationships of different photoperiodic responses of the two cultivars and the expression of photoperiod pathway genes were analyzed accordingly. The photoperiod insensitive（PI） genotype plants flower early under SD; meanwhile, the abnormal expression of the Ppd-D1 a allele is accompanied with an increase in Ta FT1 expression and the TaCO expression variation. The results would facilitate molecular breeding in wheat.
基金National Key Research and Development(R&D)Program Project,No.2019YFC1315705.
文摘BACKGROUND Colorectal cancer(CRC)is one of the most malignant gastrointestinal cancers worldwide.The liver is the most important metastatic target organ,and liver metastasis is the leading cause of death in patients with CRC.Owing to the lack of sensitive biomarkers and unclear molecular mechanism,the occurrence of liver metastases cannot be predicted and the clinical outcomes are bad for liver metastases.Therefore,it is very important to identify the diagnostic or prognostic markers for liver metastases of CRC.AIM To investigate the highly differentially expressed genes(HDEGs)and prognostic marker for liver metastases of CRC.METHODS Data from three NCBI Gene Expression Omnibus(GEO)datasets were used to show HDEGs between liver metastases of CRC and tumour or normal samples.These significantly HDEGs of the three GEO datasets take the interactions.And these genes were screened through an online tool to explore the prognostic value.Then,TIMER and R package were utilized to investigate the immunity functions of the HDEGs and gene set enrichment analysis was used to explore their potential functions.RESULTS Based on the selection criteria,three CRC datasets for exploration(GSE14297,GSE41258,and GSE49355)were chosen.Venn diagrams were used to show HDEGs common to the six groups and 47 HDEGs were obtained.The HDEGs were shown by using STRING and Cytoscape software.Based on the TCGA database,APOC1 showed significantly different expression between N2 and N0,and N2 and N1.And there was also a significant difference in expression between T2 and T4,and between T2 and T3.In 20 paired CRC and normal tissues,quantitative real-time polymerase chain reaction illustrated that the APOC1 mRNA was strongly upregulated in CRC tissues(P=0.014).PrognoScan and GEPIA2 revealed the prognostic value of APOC1 for overall survival and diseasefree survival in CRC(P<0.05).TIMER showed that APOC1 has a close relationship with immune infiltration(P<0.05).CONCLUSION APOC1 is a biomarker that is associated with both the diagnosis and prognosis of liver metastases of CRC.
基金supported by the National Key R&D Program of China(2018YFD0100903)the China Agriculture Research System of MOF and MARA(CARS-02-13)the Natural Science Fund of Liaoning Province,China(20170540806)。
文摘Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance.This study evaluated four traits(mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12)related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms(SNPs).The genomewide association study detected that 273 SNPs were in linkage disequilibrium(LD)with the genetic basis of maize deep-sowing tolerance.The RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes(DEGs)in two comparisons,which shared 281 DEGs.By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs,we identified seven candidate genes,of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein.GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length,auxin,or light response.Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length.Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines.These results suggest that GRMZM2G119769 is the most likely candidate gene.This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes,which would be useful for further research on maize deep-sowing tolerance.
基金National Natural Science Foundation of China(30972184,31272574).
文摘[Objectives]This study was conducted to determine the functions of eight ORF genes of porcine circovirus-like virus P1.[Methods]The double-copy tandem molecular cloning of porcine circovirus-like virus P1 genome was used to construct molecular clones with eight ORFs deleted by DNA site-directed mutagenesis technology.After transfected into PK15 cells for a certain period of time,RNA were extracted and was used to verify whether the eight ORFs were deleted or not and used for gene microarry analysis.The GO functions and KEGG pathway enrichment of differentially expressed genes were analyzed.[Results]P1 ORF1 is mainly involved in the biological processes of defense response to virus,signal transduction,regulation of Rab GTPase activity,and lipid metabolic process,and involved in the molecular functions of protein phosphatase inhibitor activity,phosphatidylinositol phospholipase C activity,2 iron,2 sulfur cluster binding,phosphoric diester hydrolase activity,and Rab GTPase activator activity,and in the KEGG pathways of secretion of digestive gland and nervous system development.P1 ORF2 is mainly involved in the biological processes of positive regulation of leukocyte chemotaxis,positive regulation of cell proliferation,positive regulation of cell migration,defense response to virus,regulation of cell growth,and involved in the molecular functions of insulin-like growth factor binding,and chemokine activity,and in the KEGG pathways of cytosolic DNA-sensing pathway,RIG-I-like receptor signaling pathway,toll-like receptor signaling pathway,chemokine signaling pathway,and cytokines,cytokine-cytokine receptor interaction.The biological processes,molecular functions and related pathways involving P1 ORF3 and ORF5 are basically similar to those of ORF2.P1 ORF8 is mainly involved in the biological processes of purine ribonucleotide biosynthetic process,amino acid transport,defense response to virus,amino acid transmembrane transport,and involved in molecular functions of N6-(1,2-dicarboxyethyl)AMP AMP-lyase(fumarate-forming)activity,iron-sulfur cluster binding,amino acid transmembrane transporter activity.[Conclusions]The analysis of the ORF functions of P1 virus lays a foundation for the study of its pathogenicity and pathogenesis.
