Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophi...Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophilus),we used bioinformatics approaches to analyze genomic data for B.xylophilus and identified Bx-MRP genes.We predicted the structure and function of the genes and encoded proteins.Using bioinformatics programs to predict and analyze various properties of the predicted proteins,including hydrophobicity,transmembrane regions,phosphorylation sites,and topologically isomeric structures,of these Bx-MRP genes,we determined that they function in transmembrane transport.From the results of RT-qPCR,the Bx-MRP family members confer significant differential resistance to different drug treatments.After treatment with different concentrations of emamectin benzoate,avermectin and matrine,the expression of each gene increased with increasing drug concentrations,indicating that the family members play a positive role in the regulation of multidrug resistance.展开更多
Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPor...Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPortal databases to analyze the expression and mutation of TOP2αand its co-expressed genes in HCC tissues.GO function and KEGG pathway enrichment of TOP2αand its co-expressed genes were identified.The TIMER database was used to analyze infiltration levels of immune cells in HCC.The impacts of TOP2αand its co-expression genes and the infiltrated immune cells on the survival of HCC patients were assayed by Kaplan-Meier plotter analysis.Results TOP2αand its co-expression genes were highly expressed in HCC(P<0.001)and detrimental to overall survival of HCC patients(P<0.001).TOP2αand its co-expression genes were mainly involved in cell mitosis and proliferation,and cell cycle pathway(ID:hsa04110,P=0.001945).TOP2αand its co-expression genes were mutated in HCC and the mutations were significantly detrimental to overall survival(P=0.0247)and disease-free survival(P=0.0265)of HCC patients.High TOP2αexpression was positively correlated with the infiltration of B cell(r=0.459,P<0.01),CD8^(+)T cell(r=0.312,P<0.01),CD4^(+)T cell(r=0.370,P<0.01),macrophage(r=0.459,P<0.01),neutrophil(r=0.405,P<0.01),and dendritic cell(r=0.473,P<0.01)in HCC.The CD8^(+)T cell infiltration significantly prolonged the 3-and 5-year survival of HCC patients(all P<0.05),and CD4^(+)T cell infiltration significantly shortened the 3-,5-,and 10-year survival of HCC patients(all P<0.05).Conclusion TOP2αmay be an oncogene,which was associated with poor prognosis of HCC patients and could be used as a biomarker for the prognostic prediction of HCC.展开更多
Bacillus velezensis is a Gram-positive and spore-forming bacterium.It has potent antimicrobial properties that can be used to promote plant growth and as a pesticide by inhibiting pathogens.B.velezensis has the capabi...Bacillus velezensis is a Gram-positive and spore-forming bacterium.It has potent antimicrobial properties that can be used to promote plant growth and as a pesticide by inhibiting pathogens.B.velezensis has the capability to generate a diverse range of enzymes that have potential applications in various fields,such as enzyme production,fermented food,degradation of pollutants,and bioenergy.In addition,B.velezensis is a promising probiotic.It possesses high bile-salt tolerance characteristics and has a high success rate of colonization in the intestinal mucosa.Besides,the strain can also regulate gut microbiota constitute by increasing the number of beneficial microorganisms and decreasing the number of pathogens.Furthermore,based on its special properties,including high-yield protease production and high salt-tolerance,B.velezensis shows potential for use in marine protein fermentation,opening up new avenues for the development of novel food products and bioactive peptides.In addition,B.velezensis can shorten the fermentation time as well as improve the nutritional value and flavor of fermented food.The safety of B.velezensis for food production was evaluated.This review provides valuable insights into the potential uses and benefits of B.velezensis,particularly in the context of fermented foods.展开更多
BACKGROUND:The molecular mechanism of sepsis-associated acute kidney injury(SA-AKI)is unclear.We analyzed co-differentially expressed genes(co-DEGs)to elucidate the underlying mechanism and intervention targets of SA-...BACKGROUND:The molecular mechanism of sepsis-associated acute kidney injury(SA-AKI)is unclear.We analyzed co-differentially expressed genes(co-DEGs)to elucidate the underlying mechanism and intervention targets of SA-AKI.METHODS:The microarray datasets GSE65682,GSE30718,and GSE174220 were downloaded from the Gene Expression Omnibus(GEO)database.We identified the co-DEGs and constructed a gene co-expression network to screen the hub genes.We analyzed immune correlations and disease correlations and performed functional annotation of the hub genes.We also performed single-cell and microenvironment analyses and investigated the enrichment pathways and the main transcription factors.Finally,we conducted a correlation analysis to evaluate the role of the hub genes.RESULTS:Interleukin 32(IL32)was identified as the hub gene in SA-AKI,and the main enriched signaling pathways were associated with hemopoiesis,cellular response to cytokine stimulus,inflammatory response,and regulation of kidney development.Additionally,IL32 was significantly associated with mortality in SA-AKI patients.Monocytes,macrophages,T cells,and NK cells were closely related to IL32 and were involved in the immune microenvironment in SA-AKI patients.IL32 expression increased significantly in the kidney of septic mouse.Toll-like receptor 2(TLR2)was significantly and negatively correlated with IL32.CONCLUSION:IL32 is the key gene involved in SA-AKI and is significantly associated with prognosis.TLR2 and relevant immune cells are closely related to key genes.展开更多
Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were ava...Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database:GSE12606,GSE36895 and GSE66272.The differentially expressed genes were screened with GEO2R and J Venn online tools.Functional annotation including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)was applied to identify the possible function of the hub genes involved in prognosis of ccRCC.In protein protein interaction network(PPI network),the STRING online tool was used to visualize the network of the differentially expressed genes,and the core gene was selected by MCODE App in Cytoscape software.Finally,GEPIA Survival Plot was performed to assess genes associated with worse survival.Results We totally found 648 diflerentially expressed genes,including 222 up-regulated genes and 426 down-regulated genes.PPI network showed that in 28 up-regulated genes 7(CCNE2,CDK1,CDC6,CCNB2,BUB1,TTK and PTTG1)enriched in cell cycle and 4 genes(CCNE2,CDK1,CCNB2 and RRM2)enriched in p53 signaling pathway.GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1,CCNB2,RRM2t BUB1,and PTTG1 had a worse survival.GEPIA Box Plot showed that BUB1,CCNB2,PTTG1,and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues(P<O.OS).Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1,CCNB2,PTTG1,and RRM2 might manifest a poor prognosis.展开更多
Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughp...Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle.展开更多
Taxol(Paclitaxel),an important anticancer drug,is derived at very low yields from Taxus(yew)species that grow very slowly.In the present study,thirteen genes that encode enzymes involved in Taxol biosynthesis in Taxus...Taxol(Paclitaxel),an important anticancer drug,is derived at very low yields from Taxus(yew)species that grow very slowly.In the present study,thirteen genes that encode enzymes involved in Taxol biosynthesis in Taxus spp.were analyzed with bioinformatics methods,and their expression levels in different tissues and after cold and hormone treatments were also analyzed.The results indicated that many cis-elements related to abiotic stresses and hormones were found in the promoter sequences of the 8 genes involved in Taxol biosynthesis.Moreover,the 13 enzymes encoded by the target genes were located in different organelles and had many phosphorylation sites in the response proteins.The 13 genes were expressed highly either in roots or in stems,with lower transcripts in needles,and they were highly expressed after treatment with cold,gibberellin,methyl jasmonate or coronatine,consistent with predictions based on the bioinformatics analysis.These results suggest that the factors such as hormones and abiotic stresses stimulate taxane biosynthesis in yews,providing an important way to sustainably generate taxanes from yew trees or their cell cultures to improve Taxol yields.展开更多
The full-length cDNA of 909 bp of the osteopontin gene(OPN) was isolated from of Large White Pig and analyzed with bioinformatics methods.The results showed high proportions of Asp,Glu and Ser and verified presence of...The full-length cDNA of 909 bp of the osteopontin gene(OPN) was isolated from of Large White Pig and analyzed with bioinformatics methods.The results showed high proportions of Asp,Glu and Ser and verified presence of the special sequence Arg-Gly-Asp(RGD) in the primary structure of OPN.There were high proportions of alpha helices and strong hydrophilicity in the secondary structure. The signature sequence of OPN([KQ]-x-[TA]-x(2)-[GA]-S-S-E-E-K) was located in the first region of high homology.Two phylogenetic trees were constructed,based on the entire OPN protein sequence and the conserved signature sequence,and showed that the relationship between pig and cow was the closest, but farthest between pig and chicken.OPN mRNA was expressed in many tissues of the pig:higher in the stomach,kidney,lung,small intestine and ovary,and lower in the heart,spleen and large intestine.The OPN protein size differed in different tissues:70 kDa in liver and muscle,70 and 45 kDa in stomach,small intestines and kidney,70,45 and 24 kDa in lung,heart and uterus.展开更多
The NAC transcription factor family is plant-specific with various biological functions.However,there are few studies on the NAC gene involving coniferous species.Bioinformatics research and expression analysis of NAC...The NAC transcription factor family is plant-specific with various biological functions.However,there are few studies on the NAC gene involving coniferous species.Bioinformatics research and expression analysis of NAC genes in Larix olgensis can be used to analyse the function of the NAC gene in the future.Screening of excellent genetic materials and molecular breeding have been utilized to cultivate high-quality,stress-resistant larches.According to the transcriptome data for L.olgensis,the genes Uni-gene81490 and Unigene70699 with complete ORFs(open reading frames)were obtained by conserved domain analy-sis and named LoNAC1 and LoNAC2,respectively.The cDNAs of LoNAC1 and LoNAC2 were 1971 bp and 1095 bp in length,encoding 656 and 364 amino acids,respectively.The molecular weights of the proteins encoded by the two genes were predicted to be 72.61 kDa and 41.13 kDa,and subcellular localization analysis indicated that the proteins were concentrated in the nucleus.The results of real-time quantitative PCR analysis showed that at different growth stages and in different tissues of L.olgensis,the relative expression levels of the two NAC genes were highest in the stem,and the expression differences were more obvious in non-lignified tissues.After drought,salt and alkali stress and hormone treatment,expression was induced to different degrees.The expression levels of LoNAC1 and LoNAC2 in semi-lignified L.olgensis were higher than in the other two periods(non-lignified and lignified),and expression levels significantly increased under drought and salt stress.Relative expression levels changed under hormone treatment.It is speculated that these two genes may not only be related to drought and salt stress and secondary growth but may also be induced by hormones such as abscisic acid.Overall,LoNAC1 and LoNAC2 are genetic materials that can be used for molecular breeding of larch.展开更多
A fault sensitivity analysis（FSA）-resistance model based on time randomization is proposed.The randomization unit is composed of two parts,namely the configurable register array（R-A）and the decoder（chiefly random...A fault sensitivity analysis（FSA）-resistance model based on time randomization is proposed.The randomization unit is composed of two parts,namely the configurable register array（R-A）and the decoder（chiefly random number generator,RNG）.In this way,registers chosen can be either valid or invalid depending on the configuration information generated by the decoder.Thus,the fault sensitivity information can be confusing.Meanwhile,based on this model,a defensive scheme is designed to resist both fault sensitivity analysis（FSA）and differential power analysis（DPA）.This scheme is verified with our experiments.展开更多
近年来全球极端低温天气频发,严重影响了茶树的产量和品质。ICE(Inducer of CBF expression)基因家族主要参与植物的低温胁迫响应,但在茶树领域中的相关研究还不够全面。本研究从茶树基因组中鉴定出51个茶树CsICEs基因,对其理化性质、...近年来全球极端低温天气频发,严重影响了茶树的产量和品质。ICE(Inducer of CBF expression)基因家族主要参与植物的低温胁迫响应,但在茶树领域中的相关研究还不够全面。本研究从茶树基因组中鉴定出51个茶树CsICEs基因,对其理化性质、基因结构和启动子顺式作用元件展开生物信息学分析。茶树CsICEs基因的启动子区域富含光响应、植物激素、生长发育及非生物胁迫相关顺式作用元件,其可能参与多种逆境胁迫响应。转录组分析和RT-qPCR验证结果发现,低温下CsICE43基因的表达量上升了4.24倍,其可能与茶树低温响应相关。以茶树品种‘保靖黄金茶1号’的cDNA为模板,克隆获得了CsICE43基因,其在不同组织中的表达模式存在差异,在顶芽和嫩叶中特异性高表达。蛋白氨基酸序列和系统进化树分析表明,CsICE43基因包含与ICE家族其他成员一致的S-rich、bHLH、ACT等保守结构域,且与毛花猕猴桃(Actinidiaeriantha)的亲缘关系较近。在STRING在线网站中以拟南芥AtICEs为模型,推测茶树CsICE43蛋白与HOS1、MYB15、DREB1/2存在潜在的互作关系。亚细胞定位试验表明CsICE43定位于细胞核,与跨膜结构分析结果一致。综上所述,本研究发现CsICE43基因可能与茶树低温响应关联,为深入挖掘其基因功能与抗寒分子机理提供了一定的理论基础。展开更多
[目的]探讨鸡热休克蛋白8(heat shock protein family A member 8,HSPA8)的生物学特性及其在应激状态下胸腺中的表达模式。[方法]试验以固始鸡胸腺为材料,利用PCR技术扩增并克隆HSPA8基因CDS区,通过生物信息学方法分析其生物学特性和结...[目的]探讨鸡热休克蛋白8(heat shock protein family A member 8,HSPA8)的生物学特性及其在应激状态下胸腺中的表达模式。[方法]试验以固始鸡胸腺为材料,利用PCR技术扩增并克隆HSPA8基因CDS区,通过生物信息学方法分析其生物学特性和结构特点,并检测其在不同组织中的相对表达量。构建断喙应激和热应激模型,采用实时荧光定量PCR技术检测炎症因子和HSPA8基因在不同应激模型鸡胸腺中的表达情况。[结果]鸡HSPA8基因CDS区长度为1 941 bp,共编码氨基酸646个,与红原鸡基因序列相似性为98.92%;HSPA8基因核苷酸序列的系统发育树结果表明,固始鸡与火鸡亲缘关系最近,与哺乳动物次之,与低等鱼类亲缘关系最远;HSPA8蛋白属于酸性蛋白,稳定性和亲水性强,不属于分泌蛋白且无跨膜结构域,有多个磷酸化和糖基化修饰位点,主要在细胞核内发挥作用,具有2个保守性结构域,与DNAJC5、HSPB1、DNAJA1和GAK等蛋白存在相互作用;HSAP8基因在雏鸡各组织中广泛表达,其中在胰腺中表达量最高,在胸肌中表达量最低;应激模型评价结果发现,断喙应激和热应激导致鸡血清皮质酮、白细胞介素-6(IL-6)和肿瘤坏死因子-α(TNF-α)等含量显著增加(P<0.05),T细胞亚群(CD3^(+))和免疫球蛋白G(IgG)含量有所降低;断喙应激模型鸡胸腺中IL-1β、IL-6、TNF-α和IL-8基因表达量在第1天显著升高(P<0.05),第5天显著降低(P<0.05);热应激模型鸡胸腺中IL-1β、IL-6、TNF-α和IL-8基因表达量显著升高(P<0.05);HSPA8基因在断喙后第1和3天胸腺中表达量显著升高(P<0.05),第5天显著降低(P<0.05);在持续热应激组中显著降低(P<0.05)。[结论]HSPA8基因参与鸡胸腺应激性免疫应答反应,可作为反映家禽是否处于应激性免疫抑制状态的可靠指标。以上结果为进一步研究HSPA8的免疫调控功能提供参考依据。展开更多
基金supported by the National Key Research and Development Program of China(2017YFD0600101).
文摘Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophilus),we used bioinformatics approaches to analyze genomic data for B.xylophilus and identified Bx-MRP genes.We predicted the structure and function of the genes and encoded proteins.Using bioinformatics programs to predict and analyze various properties of the predicted proteins,including hydrophobicity,transmembrane regions,phosphorylation sites,and topologically isomeric structures,of these Bx-MRP genes,we determined that they function in transmembrane transport.From the results of RT-qPCR,the Bx-MRP family members confer significant differential resistance to different drug treatments.After treatment with different concentrations of emamectin benzoate,avermectin and matrine,the expression of each gene increased with increasing drug concentrations,indicating that the family members play a positive role in the regulation of multidrug resistance.
基金This work was partially supported by the Key Project of Natural Science Research of Education Department of Anhui Province(No.KJ2019A0338)Industry-University Cooperation Project of the Ministry of Education(No.202101160001).
文摘Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPortal databases to analyze the expression and mutation of TOP2αand its co-expressed genes in HCC tissues.GO function and KEGG pathway enrichment of TOP2αand its co-expressed genes were identified.The TIMER database was used to analyze infiltration levels of immune cells in HCC.The impacts of TOP2αand its co-expression genes and the infiltrated immune cells on the survival of HCC patients were assayed by Kaplan-Meier plotter analysis.Results TOP2αand its co-expression genes were highly expressed in HCC(P<0.001)and detrimental to overall survival of HCC patients(P<0.001).TOP2αand its co-expression genes were mainly involved in cell mitosis and proliferation,and cell cycle pathway(ID:hsa04110,P=0.001945).TOP2αand its co-expression genes were mutated in HCC and the mutations were significantly detrimental to overall survival(P=0.0247)and disease-free survival(P=0.0265)of HCC patients.High TOP2αexpression was positively correlated with the infiltration of B cell(r=0.459,P<0.01),CD8^(+)T cell(r=0.312,P<0.01),CD4^(+)T cell(r=0.370,P<0.01),macrophage(r=0.459,P<0.01),neutrophil(r=0.405,P<0.01),and dendritic cell(r=0.473,P<0.01)in HCC.The CD8^(+)T cell infiltration significantly prolonged the 3-and 5-year survival of HCC patients(all P<0.05),and CD4^(+)T cell infiltration significantly shortened the 3-,5-,and 10-year survival of HCC patients(all P<0.05).Conclusion TOP2αmay be an oncogene,which was associated with poor prognosis of HCC patients and could be used as a biomarker for the prognostic prediction of HCC.
基金financially supported by the Public Welfare Project of Zhoushan City,Zhejiang(2022C31050)。
文摘Bacillus velezensis is a Gram-positive and spore-forming bacterium.It has potent antimicrobial properties that can be used to promote plant growth and as a pesticide by inhibiting pathogens.B.velezensis has the capability to generate a diverse range of enzymes that have potential applications in various fields,such as enzyme production,fermented food,degradation of pollutants,and bioenergy.In addition,B.velezensis is a promising probiotic.It possesses high bile-salt tolerance characteristics and has a high success rate of colonization in the intestinal mucosa.Besides,the strain can also regulate gut microbiota constitute by increasing the number of beneficial microorganisms and decreasing the number of pathogens.Furthermore,based on its special properties,including high-yield protease production and high salt-tolerance,B.velezensis shows potential for use in marine protein fermentation,opening up new avenues for the development of novel food products and bioactive peptides.In addition,B.velezensis can shorten the fermentation time as well as improve the nutritional value and flavor of fermented food.The safety of B.velezensis for food production was evaluated.This review provides valuable insights into the potential uses and benefits of B.velezensis,particularly in the context of fermented foods.
基金supported by Beijing Natural Science Foundation(No.7222162 to Dr.Hui Liu)。
文摘BACKGROUND:The molecular mechanism of sepsis-associated acute kidney injury(SA-AKI)is unclear.We analyzed co-differentially expressed genes(co-DEGs)to elucidate the underlying mechanism and intervention targets of SA-AKI.METHODS:The microarray datasets GSE65682,GSE30718,and GSE174220 were downloaded from the Gene Expression Omnibus(GEO)database.We identified the co-DEGs and constructed a gene co-expression network to screen the hub genes.We analyzed immune correlations and disease correlations and performed functional annotation of the hub genes.We also performed single-cell and microenvironment analyses and investigated the enrichment pathways and the main transcription factors.Finally,we conducted a correlation analysis to evaluate the role of the hub genes.RESULTS:Interleukin 32(IL32)was identified as the hub gene in SA-AKI,and the main enriched signaling pathways were associated with hemopoiesis,cellular response to cytokine stimulus,inflammatory response,and regulation of kidney development.Additionally,IL32 was significantly associated with mortality in SA-AKI patients.Monocytes,macrophages,T cells,and NK cells were closely related to IL32 and were involved in the immune microenvironment in SA-AKI patients.IL32 expression increased significantly in the kidney of septic mouse.Toll-like receptor 2(TLR2)was significantly and negatively correlated with IL32.CONCLUSION:IL32 is the key gene involved in SA-AKI and is significantly associated with prognosis.TLR2 and relevant immune cells are closely related to key genes.
基金the National Technical system of Chinese Medicinal Materials Industry(No.CARS-21)the Key Natural Science Projects of West Anhui University in China(No.WXZR201932)+4 种基金the Training Program of Innovate and Entrepreneurship of National College students in China(No.201810376058,201810376061)Anhui Provincial Natural Science Foundation in China(No.2017A030311022)Anhui Provincial University Natural Science Project in China(No.KJ2018A0413,KJ2017a407)Anhui Provincial Quality of Undergraduate project in China(No.2018zygc075,2018jyxm1153,2018jyxm1155)the Teaching and Research Projects of West Anhui University in China(No.wxxy2018026).
文摘Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database:GSE12606,GSE36895 and GSE66272.The differentially expressed genes were screened with GEO2R and J Venn online tools.Functional annotation including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)was applied to identify the possible function of the hub genes involved in prognosis of ccRCC.In protein protein interaction network(PPI network),the STRING online tool was used to visualize the network of the differentially expressed genes,and the core gene was selected by MCODE App in Cytoscape software.Finally,GEPIA Survival Plot was performed to assess genes associated with worse survival.Results We totally found 648 diflerentially expressed genes,including 222 up-regulated genes and 426 down-regulated genes.PPI network showed that in 28 up-regulated genes 7(CCNE2,CDK1,CDC6,CCNB2,BUB1,TTK and PTTG1)enriched in cell cycle and 4 genes(CCNE2,CDK1,CCNB2 and RRM2)enriched in p53 signaling pathway.GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1,CCNB2,RRM2t BUB1,and PTTG1 had a worse survival.GEPIA Box Plot showed that BUB1,CCNB2,PTTG1,and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues(P<O.OS).Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1,CCNB2,PTTG1,and RRM2 might manifest a poor prognosis.
基金Fund supported by the National Natural Science Foundation of China(81460598 and 81660644)the Natural Science Foundation of Jiangsu Province(BK20170267)Guangxi Special Fund for the First-Class Discipline Construction Project(05019038).
文摘Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle.
基金This work was supported by National Natural Science Foundation of China(31570675)a Grant from the National Key Research and Development Program of China(2017YFD060070605)a Grant for National non-profit Research Institutions of Chinese Academy of Forestry(CAFYBB2018SY009).
文摘Taxol(Paclitaxel),an important anticancer drug,is derived at very low yields from Taxus(yew)species that grow very slowly.In the present study,thirteen genes that encode enzymes involved in Taxol biosynthesis in Taxus spp.were analyzed with bioinformatics methods,and their expression levels in different tissues and after cold and hormone treatments were also analyzed.The results indicated that many cis-elements related to abiotic stresses and hormones were found in the promoter sequences of the 8 genes involved in Taxol biosynthesis.Moreover,the 13 enzymes encoded by the target genes were located in different organelles and had many phosphorylation sites in the response proteins.The 13 genes were expressed highly either in roots or in stems,with lower transcripts in needles,and they were highly expressed after treatment with cold,gibberellin,methyl jasmonate or coronatine,consistent with predictions based on the bioinformatics analysis.These results suggest that the factors such as hormones and abiotic stresses stimulate taxane biosynthesis in yews,providing an important way to sustainably generate taxanes from yew trees or their cell cultures to improve Taxol yields.
基金supported by Scientific and Technological Project in Heilongjiang Province (GB05B 106)Postdoctoral Fund of Heilongjiang Province(LRB07-392)
文摘The full-length cDNA of 909 bp of the osteopontin gene(OPN) was isolated from of Large White Pig and analyzed with bioinformatics methods.The results showed high proportions of Asp,Glu and Ser and verified presence of the special sequence Arg-Gly-Asp(RGD) in the primary structure of OPN.There were high proportions of alpha helices and strong hydrophilicity in the secondary structure. The signature sequence of OPN([KQ]-x-[TA]-x(2)-[GA]-S-S-E-E-K) was located in the first region of high homology.Two phylogenetic trees were constructed,based on the entire OPN protein sequence and the conserved signature sequence,and showed that the relationship between pig and cow was the closest, but farthest between pig and chicken.OPN mRNA was expressed in many tissues of the pig:higher in the stomach,kidney,lung,small intestine and ovary,and lower in the heart,spleen and large intestine.The OPN protein size differed in different tissues:70 kDa in liver and muscle,70 and 45 kDa in stomach,small intestines and kidney,70,45 and 24 kDa in lung,heart and uterus.
基金This project was supported by the National Science and Technology Major Project(2018ZX08020003-001-001)the National Natural Science Foundation of China(Grant No.31700595)+1 种基金the Fundamental Research Funds for the Central Universities(2572019BA13)Heilongjiang Touyan Innovation Team Program.
文摘The NAC transcription factor family is plant-specific with various biological functions.However,there are few studies on the NAC gene involving coniferous species.Bioinformatics research and expression analysis of NAC genes in Larix olgensis can be used to analyse the function of the NAC gene in the future.Screening of excellent genetic materials and molecular breeding have been utilized to cultivate high-quality,stress-resistant larches.According to the transcriptome data for L.olgensis,the genes Uni-gene81490 and Unigene70699 with complete ORFs(open reading frames)were obtained by conserved domain analy-sis and named LoNAC1 and LoNAC2,respectively.The cDNAs of LoNAC1 and LoNAC2 were 1971 bp and 1095 bp in length,encoding 656 and 364 amino acids,respectively.The molecular weights of the proteins encoded by the two genes were predicted to be 72.61 kDa and 41.13 kDa,and subcellular localization analysis indicated that the proteins were concentrated in the nucleus.The results of real-time quantitative PCR analysis showed that at different growth stages and in different tissues of L.olgensis,the relative expression levels of the two NAC genes were highest in the stem,and the expression differences were more obvious in non-lignified tissues.After drought,salt and alkali stress and hormone treatment,expression was induced to different degrees.The expression levels of LoNAC1 and LoNAC2 in semi-lignified L.olgensis were higher than in the other two periods(non-lignified and lignified),and expression levels significantly increased under drought and salt stress.Relative expression levels changed under hormone treatment.It is speculated that these two genes may not only be related to drought and salt stress and secondary growth but may also be induced by hormones such as abscisic acid.Overall,LoNAC1 and LoNAC2 are genetic materials that can be used for molecular breeding of larch.
文摘A fault sensitivity analysis（FSA）-resistance model based on time randomization is proposed.The randomization unit is composed of two parts,namely the configurable register array（R-A）and the decoder（chiefly random number generator,RNG）.In this way,registers chosen can be either valid or invalid depending on the configuration information generated by the decoder.Thus,the fault sensitivity information can be confusing.Meanwhile,based on this model,a defensive scheme is designed to resist both fault sensitivity analysis（FSA）and differential power analysis（DPA）.This scheme is verified with our experiments.
文摘近年来全球极端低温天气频发,严重影响了茶树的产量和品质。ICE(Inducer of CBF expression)基因家族主要参与植物的低温胁迫响应,但在茶树领域中的相关研究还不够全面。本研究从茶树基因组中鉴定出51个茶树CsICEs基因,对其理化性质、基因结构和启动子顺式作用元件展开生物信息学分析。茶树CsICEs基因的启动子区域富含光响应、植物激素、生长发育及非生物胁迫相关顺式作用元件,其可能参与多种逆境胁迫响应。转录组分析和RT-qPCR验证结果发现,低温下CsICE43基因的表达量上升了4.24倍,其可能与茶树低温响应相关。以茶树品种‘保靖黄金茶1号’的cDNA为模板,克隆获得了CsICE43基因,其在不同组织中的表达模式存在差异,在顶芽和嫩叶中特异性高表达。蛋白氨基酸序列和系统进化树分析表明,CsICE43基因包含与ICE家族其他成员一致的S-rich、bHLH、ACT等保守结构域,且与毛花猕猴桃(Actinidiaeriantha)的亲缘关系较近。在STRING在线网站中以拟南芥AtICEs为模型,推测茶树CsICE43蛋白与HOS1、MYB15、DREB1/2存在潜在的互作关系。亚细胞定位试验表明CsICE43定位于细胞核,与跨膜结构分析结果一致。综上所述,本研究发现CsICE43基因可能与茶树低温响应关联,为深入挖掘其基因功能与抗寒分子机理提供了一定的理论基础。
文摘[目的]探讨鸡热休克蛋白8(heat shock protein family A member 8,HSPA8)的生物学特性及其在应激状态下胸腺中的表达模式。[方法]试验以固始鸡胸腺为材料,利用PCR技术扩增并克隆HSPA8基因CDS区,通过生物信息学方法分析其生物学特性和结构特点,并检测其在不同组织中的相对表达量。构建断喙应激和热应激模型,采用实时荧光定量PCR技术检测炎症因子和HSPA8基因在不同应激模型鸡胸腺中的表达情况。[结果]鸡HSPA8基因CDS区长度为1 941 bp,共编码氨基酸646个,与红原鸡基因序列相似性为98.92%;HSPA8基因核苷酸序列的系统发育树结果表明,固始鸡与火鸡亲缘关系最近,与哺乳动物次之,与低等鱼类亲缘关系最远;HSPA8蛋白属于酸性蛋白,稳定性和亲水性强,不属于分泌蛋白且无跨膜结构域,有多个磷酸化和糖基化修饰位点,主要在细胞核内发挥作用,具有2个保守性结构域,与DNAJC5、HSPB1、DNAJA1和GAK等蛋白存在相互作用;HSAP8基因在雏鸡各组织中广泛表达,其中在胰腺中表达量最高,在胸肌中表达量最低;应激模型评价结果发现,断喙应激和热应激导致鸡血清皮质酮、白细胞介素-6(IL-6)和肿瘤坏死因子-α(TNF-α)等含量显著增加(P<0.05),T细胞亚群(CD3^(+))和免疫球蛋白G(IgG)含量有所降低;断喙应激模型鸡胸腺中IL-1β、IL-6、TNF-α和IL-8基因表达量在第1天显著升高(P<0.05),第5天显著降低(P<0.05);热应激模型鸡胸腺中IL-1β、IL-6、TNF-α和IL-8基因表达量显著升高(P<0.05);HSPA8基因在断喙后第1和3天胸腺中表达量显著升高(P<0.05),第5天显著降低(P<0.05);在持续热应激组中显著降低(P<0.05)。[结论]HSPA8基因参与鸡胸腺应激性免疫应答反应,可作为反映家禽是否处于应激性免疫抑制状态的可靠指标。以上结果为进一步研究HSPA8的免疫调控功能提供参考依据。
