Objective:To uncover the underlying mechanisms of action of the Yinlai decoction on high-calorie dietinduced pneumonia through proteomics analysis.Methods:Based on the Gene Expression Omnibus(GEO)database,lung tissue ...Objective:To uncover the underlying mechanisms of action of the Yinlai decoction on high-calorie dietinduced pneumonia through proteomics analysis.Methods:Based on the Gene Expression Omnibus(GEO)database,lung tissue samples from normal and high-fat diet(HFD)fed mice in the GSE16377 dataset were selected as test cohorts to identify differentially expressed genes and conduct bioinformatics analyses.In the animal experiments,mice were randomly divided into the control(N),high-calorie diet pneumonia(M),and Yinlai decoction treatment(Y)groups.Mice in the M group received high-calorie feed and a 0.5 mg/mL lipopolysaccharide solution spray for 30 min for 3 d.The mice in the Y group were intragastrically administered 2 mL/10 g Yinlai decoction twice daily for 3 d.Pathological evaluation of the lung tissue was performed.Differentially expressed proteins(DEPs)in the lung tissue were identified using quantitative proteomics and bioinformatics analyses.The drug-target relationships between Yinlai decoction and core DEPs in the lung tissue were verified using AutoDock Vina and Molecular Graphics Laboratory(MGL)Tools.DEPs were verified by western blot.Results:GEO data mining showed that an HFD altered oxidative phosphorylation in mouse lung tissue.The Yinlai decoction alleviated pathological damage to lung tissue and pneumonia in mice that were fed a high-calorie diet.A total of 47 DEPs were identified between the Y and M groups.Enrichment analysis revealed their association with energy metabolism pathways such as the tricarboxylic acid cycle(TCA)and oxidative phosphorylation.The protein-protein interaction network revealed that Atp5a1,Pdha1,and Sdha were the target proteins mediating the therapeutic effects of Yinlai decoction.Molecular docking results suggested that the mechanism of the therapeutic effect of Yinlai decoction involves the binding of brassinolide,praeruptorin B,chrysoeriol,and other components in Yinlai decoction to Atp5a1.Conclusion:The Yinlai decoction alleviated lung tissue damage and pneumonia in mice that were fed a high-calorie diet by regulating the TCA and oxidative phosphorylation.Our study highlights the importance of a healthy diet for patients with pneumonia and provides a scientific basis for the prevention and treatment of pneumonia through dietary adjustments.展开更多
目的基于放射性核素标记相对与绝对定量技术(isobaric tags for relative and absolute quantitation,iTRAQ)探究化疗相关认知障碍(chemotherapy-induced cognitive impairment,CICI)的发生机制。方法雄性SD大鼠6只,随机分为对照组和化...目的基于放射性核素标记相对与绝对定量技术(isobaric tags for relative and absolute quantitation,iTRAQ)探究化疗相关认知障碍(chemotherapy-induced cognitive impairment,CICI)的发生机制。方法雄性SD大鼠6只,随机分为对照组和化疗组,化疗组大鼠静脉注射环磷酰胺和阿霉素,每周1次,共3周;对照组大鼠给予等剂量的0.9%NaCl注射液。通过iTRAQ技术探究两组间的差异蛋白,根据GO和KEGG数据库分析对差异蛋白的生物功能及相关信号通路进行富集。结果蛋白质组学共鉴定出52764条肽段和7670个蛋白,化疗组与对照组的差异蛋白为434种,其中显著下调蛋白338种,显著上调蛋白96种。结果显示差异蛋白主要富集于细胞器、细胞膜等细胞成分;主要参与细胞代谢、生物调节及代谢等生物学过程;显著富集于结合、催化等分子功能。对差异蛋白进行KEGG信号通路富集分析显示其主要富集于单纯疱疹病毒感染、免疫排斥、自身免疫性甲状腺疾病等与免疫相关的通路。通过构建蛋白-蛋白相互作用(protein-protein interaction,PPI)网络发现信号转导及转录激活因子(signal transducer and activator of transcription,STAT)及泛素样修饰剂ISG15处于中心位置,均与免疫相关。结论本研究利用iTRAQ技术CICI的可能机制进行探究,结果进一步说明CICI可能与神经炎症有关,特别是其与自身免疫的相关性值得进一步研究。γ干扰素(interferonγ,IFN-γ)可能是CICI潜在的生物学标志物及治疗靶点。展开更多
【目的】远缘杂交育种是目前牡丹、芍药品种改良和育种的主要方法,而远缘杂交不亲和一直是制约其快速发展的主要因素。本研究从牡丹、芍药远缘杂交授粉后不亲和应答相关的柱头差异蛋白与转录组方面深入研究,揭示牡丹、芍药远缘杂交不亲...【目的】远缘杂交育种是目前牡丹、芍药品种改良和育种的主要方法,而远缘杂交不亲和一直是制约其快速发展的主要因素。本研究从牡丹、芍药远缘杂交授粉后不亲和应答相关的柱头差异蛋白与转录组方面深入研究,揭示牡丹、芍药远缘杂交不亲和的分子机理,为杂交育种提供理论依据。【方法】以芍药‘粉玉奴’自交、芍药‘粉玉奴’与牡丹‘凤丹白’杂交为供试材料,在授粉后24 h采取柱头,分别进行同位素标记相对定量(iTRAQ)和转录组技术分析。对所获得的蛋白和转录组数据进行生物信息学分析,并对其中可能与远缘杂交不亲和相关的基因进行定量PCR验证。【结果】利用iTRAQ技术分析牡丹、芍药远缘杂交后柱头中蛋白质的表达差异,共鉴定到685个差异蛋白,富集到了188条通路,其中显著富集的Pathway有18条。与不亲和授粉相关代谢通路有RNA降解、钙信号途径、丝裂原活化蛋白激酶(mitogen-activated protein kinase signaling pathway,MAPK)信号途径、磷脂酰肌醇信号系统。在RNA降解代谢通路中,烯醇酶(Enolase)、热休克蛋白DnaK(HSP70)及病菌抗原(GroEL)均表达下调。在钙信号途径中,钙调蛋白(CALM)表达下调,腺苷酸转运酶(adenine nucleotide translocase,ANT)表达量增加,表达上调。MAPK信号途径中,乙二醛酶Ⅰ(GloI)表达下调。磷脂酰肌醇信号系统中的钙调蛋白(CALM)表达下调。随机选取与差异蛋白相关的6个基因进行qRT-PCR验证,结果显示,6个基因的表达与蛋白质水平趋势相一致,均表达下调。通过转录组测序,共获得了52998个有注释信息的Unigene,占所有Unigene的40.37%。基于6组样品的RPKM(Reads Per Kilobase per Million)值,共筛选到16224个差异基因。其中上调基因13361,下调基因2863个。对差异基因进行Pathway显著富集分析,杂交与自交相比,不亲和差异表达的基因主要富集在氧化磷酸化代谢、ABC转运蛋白、次级代谢产物等通路。与远缘杂交不亲和相关且发生显著变化的基因有CalS-5、CalS-12(胼胝质酶)和SPL(squamosa promoter binding protein-like)表达上调,ABCF(ABC transporter family protein)表达下调。【结论】在转录组和蛋白数据共注释到6个蛋白、4个基因与植物不亲和性密切相关,这些蛋白与基因可能在远缘杂交不亲和方面发挥着重要作用。展开更多
首次利用同位素标记相对和绝对定量(isobaric tags for relative and absolute quantification,iTRAQ)技术结合二维液相色谱串联质谱对草菇(Volvariella volvacea)同核和异核菌丝蛋白质组进行研究。采用QExactive质谱鉴定并经MASCOT软...首次利用同位素标记相对和绝对定量(isobaric tags for relative and absolute quantification,iTRAQ)技术结合二维液相色谱串联质谱对草菇(Volvariella volvacea)同核和异核菌丝蛋白质组进行研究。采用QExactive质谱鉴定并经MASCOT软件搜库,对所有鉴定蛋白进行主成分分析(principal component analysis,PCA)、层次聚类(hierarchical clustering)分析和GO(gene ontology)注释,并进行生物信息学分析。结果共获得2335个不同肽段,鉴定到1039个蛋白,其中1030个蛋白具有定量信息。在同核菌丝中显著上调蛋白83个,下调蛋白97个,表明iTRAQ标记技术结合二维液相色谱串联质谱可有效地分离和鉴定草菇菌丝蛋白质组。该研究结果为更深入全面地研究草菇菌丝蛋白质组学奠定基础。展开更多
橡胶树死皮(Tapping panel dryness,TPD)是限制天然橡胶产量提高的关键因子之一,鉴定健康和死皮橡胶树胶乳差异表达蛋白对阐明橡胶树死皮发生机制具有重要意义。研究首次采用同位素标记相对和绝对定量(Isobaric tags for relative and a...橡胶树死皮(Tapping panel dryness,TPD)是限制天然橡胶产量提高的关键因子之一,鉴定健康和死皮橡胶树胶乳差异表达蛋白对阐明橡胶树死皮发生机制具有重要意义。研究首次采用同位素标记相对和绝对定量(Isobaric tags for relative and absolute quantitation,iTRAQ)结合二维液相色谱串联质谱(Two-dimensional liquid chromatography-tandem mass spectrometry,2D LC-MS/MS)技术对健康和死皮橡胶树胶乳蛋白质组的差异进行研究。结果显示,有16个蛋白差异表达,其中,在死皮树中表达上调的蛋白有2个,下调的蛋白有14个。进一步应用实时荧光定量RT-PCR对其中6个差异蛋白的基因进行表达分析,发现其表达趋势与蛋白质组水平的研究结果一致。功能分析显示,这些差异蛋白主要与细胞程序性死亡(如TCTP、HSP70、CaM、cysteine protease等)和橡胶生物合成(如SRPP和diphosphomevelonate decarboxylase)相关,从蛋白质组学角度进一步验证了橡胶树死皮发生过程中涉及细胞程序性死亡和橡胶生物合成途径。展开更多
基于iTRAQ多重标记串联质谱技术系统研究脂多糖刺激下乳腺上皮细胞蛋白的差异表达,并对与乳蛋白、乳脂肪相关差异表达基因进行验证。培养纯化后的乳腺上皮细胞,经脂多糖(LPS)处理后提取细胞蛋白,采用iTRAQ标记和联合二维液相色谱-串联质...基于iTRAQ多重标记串联质谱技术系统研究脂多糖刺激下乳腺上皮细胞蛋白的差异表达,并对与乳蛋白、乳脂肪相关差异表达基因进行验证。培养纯化后的乳腺上皮细胞,经脂多糖(LPS)处理后提取细胞蛋白,采用iTRAQ标记和联合二维液相色谱-串联质谱(2D-LC-MS/MS)检测分析得到各组间细胞差异表达蛋白,并采用蛋白印迹和酶联免疫法(ELISA)对差异蛋白进行验证,然后对与乳蛋白、乳脂肪相关基因的相互作用蛋白进行PPI(Protein protein interaction)预测。乳腺上皮细胞共鉴定出2 487个蛋白,其中差异蛋白共341个,与对照组相比,163个蛋白表达上调,178个蛋白表达下调。iTRAQ测定结果显示,LPS处理组与对照组相比,αs1-酪蛋白(CSN1S1)、κ-酪蛋白(CSN3)和脂肪酸合酶(FASN)基因蛋白表达水平有统计学意义;经蛋白印迹试验结果表明,LPS诱导组αs1-酪蛋白表达水平同对照组比较,明显降低(P<0.05);应用ELISA方法测定细胞培养液中αs1-酪蛋白、κ-酪蛋白和脂肪酸合酶的浓度结果显示,LPS诱导组细胞培养液中上述蛋白的浓度明显低于对照组(P<0.05)。综上表明,LPS诱导的炎症反应可影响乳腺上皮细胞的乳蛋白和乳脂肪的合成。展开更多
基金supported by the National Natural Science Foundation of China(81874421)the Innovation Team and Talents Cultivation Program of the National Administration of Traditional Chinese Medicine(ZYYCXTD-C-202006).
文摘Objective:To uncover the underlying mechanisms of action of the Yinlai decoction on high-calorie dietinduced pneumonia through proteomics analysis.Methods:Based on the Gene Expression Omnibus(GEO)database,lung tissue samples from normal and high-fat diet(HFD)fed mice in the GSE16377 dataset were selected as test cohorts to identify differentially expressed genes and conduct bioinformatics analyses.In the animal experiments,mice were randomly divided into the control(N),high-calorie diet pneumonia(M),and Yinlai decoction treatment(Y)groups.Mice in the M group received high-calorie feed and a 0.5 mg/mL lipopolysaccharide solution spray for 30 min for 3 d.The mice in the Y group were intragastrically administered 2 mL/10 g Yinlai decoction twice daily for 3 d.Pathological evaluation of the lung tissue was performed.Differentially expressed proteins(DEPs)in the lung tissue were identified using quantitative proteomics and bioinformatics analyses.The drug-target relationships between Yinlai decoction and core DEPs in the lung tissue were verified using AutoDock Vina and Molecular Graphics Laboratory(MGL)Tools.DEPs were verified by western blot.Results:GEO data mining showed that an HFD altered oxidative phosphorylation in mouse lung tissue.The Yinlai decoction alleviated pathological damage to lung tissue and pneumonia in mice that were fed a high-calorie diet.A total of 47 DEPs were identified between the Y and M groups.Enrichment analysis revealed their association with energy metabolism pathways such as the tricarboxylic acid cycle(TCA)and oxidative phosphorylation.The protein-protein interaction network revealed that Atp5a1,Pdha1,and Sdha were the target proteins mediating the therapeutic effects of Yinlai decoction.Molecular docking results suggested that the mechanism of the therapeutic effect of Yinlai decoction involves the binding of brassinolide,praeruptorin B,chrysoeriol,and other components in Yinlai decoction to Atp5a1.Conclusion:The Yinlai decoction alleviated lung tissue damage and pneumonia in mice that were fed a high-calorie diet by regulating the TCA and oxidative phosphorylation.Our study highlights the importance of a healthy diet for patients with pneumonia and provides a scientific basis for the prevention and treatment of pneumonia through dietary adjustments.
文摘目的基于放射性核素标记相对与绝对定量技术(isobaric tags for relative and absolute quantitation,iTRAQ)探究化疗相关认知障碍(chemotherapy-induced cognitive impairment,CICI)的发生机制。方法雄性SD大鼠6只,随机分为对照组和化疗组,化疗组大鼠静脉注射环磷酰胺和阿霉素,每周1次,共3周;对照组大鼠给予等剂量的0.9%NaCl注射液。通过iTRAQ技术探究两组间的差异蛋白,根据GO和KEGG数据库分析对差异蛋白的生物功能及相关信号通路进行富集。结果蛋白质组学共鉴定出52764条肽段和7670个蛋白,化疗组与对照组的差异蛋白为434种,其中显著下调蛋白338种,显著上调蛋白96种。结果显示差异蛋白主要富集于细胞器、细胞膜等细胞成分;主要参与细胞代谢、生物调节及代谢等生物学过程;显著富集于结合、催化等分子功能。对差异蛋白进行KEGG信号通路富集分析显示其主要富集于单纯疱疹病毒感染、免疫排斥、自身免疫性甲状腺疾病等与免疫相关的通路。通过构建蛋白-蛋白相互作用(protein-protein interaction,PPI)网络发现信号转导及转录激活因子(signal transducer and activator of transcription,STAT)及泛素样修饰剂ISG15处于中心位置,均与免疫相关。结论本研究利用iTRAQ技术CICI的可能机制进行探究,结果进一步说明CICI可能与神经炎症有关,特别是其与自身免疫的相关性值得进一步研究。γ干扰素(interferonγ,IFN-γ)可能是CICI潜在的生物学标志物及治疗靶点。
文摘【目的】远缘杂交育种是目前牡丹、芍药品种改良和育种的主要方法,而远缘杂交不亲和一直是制约其快速发展的主要因素。本研究从牡丹、芍药远缘杂交授粉后不亲和应答相关的柱头差异蛋白与转录组方面深入研究,揭示牡丹、芍药远缘杂交不亲和的分子机理,为杂交育种提供理论依据。【方法】以芍药‘粉玉奴’自交、芍药‘粉玉奴’与牡丹‘凤丹白’杂交为供试材料,在授粉后24 h采取柱头,分别进行同位素标记相对定量(iTRAQ)和转录组技术分析。对所获得的蛋白和转录组数据进行生物信息学分析,并对其中可能与远缘杂交不亲和相关的基因进行定量PCR验证。【结果】利用iTRAQ技术分析牡丹、芍药远缘杂交后柱头中蛋白质的表达差异,共鉴定到685个差异蛋白,富集到了188条通路,其中显著富集的Pathway有18条。与不亲和授粉相关代谢通路有RNA降解、钙信号途径、丝裂原活化蛋白激酶(mitogen-activated protein kinase signaling pathway,MAPK)信号途径、磷脂酰肌醇信号系统。在RNA降解代谢通路中,烯醇酶(Enolase)、热休克蛋白DnaK(HSP70)及病菌抗原(GroEL)均表达下调。在钙信号途径中,钙调蛋白(CALM)表达下调,腺苷酸转运酶(adenine nucleotide translocase,ANT)表达量增加,表达上调。MAPK信号途径中,乙二醛酶Ⅰ(GloI)表达下调。磷脂酰肌醇信号系统中的钙调蛋白(CALM)表达下调。随机选取与差异蛋白相关的6个基因进行qRT-PCR验证,结果显示,6个基因的表达与蛋白质水平趋势相一致,均表达下调。通过转录组测序,共获得了52998个有注释信息的Unigene,占所有Unigene的40.37%。基于6组样品的RPKM(Reads Per Kilobase per Million)值,共筛选到16224个差异基因。其中上调基因13361,下调基因2863个。对差异基因进行Pathway显著富集分析,杂交与自交相比,不亲和差异表达的基因主要富集在氧化磷酸化代谢、ABC转运蛋白、次级代谢产物等通路。与远缘杂交不亲和相关且发生显著变化的基因有CalS-5、CalS-12(胼胝质酶)和SPL(squamosa promoter binding protein-like)表达上调,ABCF(ABC transporter family protein)表达下调。【结论】在转录组和蛋白数据共注释到6个蛋白、4个基因与植物不亲和性密切相关,这些蛋白与基因可能在远缘杂交不亲和方面发挥着重要作用。
基金国家现代农业产业技术体系建设专项资金资助(编号:CARS 24)supported by the Engineering Research Center of EdibleFungi of Fujian Province,National ImprovementCenter of Edible Fungi Varieties(Fujian Subcenter)and the Institute of Biochemistry and Cell Biology,Shanghai Institute for Biological Science,Chinese Academy of Sciences~~
文摘首次利用同位素标记相对和绝对定量(isobaric tags for relative and absolute quantification,iTRAQ)技术结合二维液相色谱串联质谱对草菇(Volvariella volvacea)同核和异核菌丝蛋白质组进行研究。采用QExactive质谱鉴定并经MASCOT软件搜库,对所有鉴定蛋白进行主成分分析(principal component analysis,PCA)、层次聚类(hierarchical clustering)分析和GO(gene ontology)注释,并进行生物信息学分析。结果共获得2335个不同肽段,鉴定到1039个蛋白,其中1030个蛋白具有定量信息。在同核菌丝中显著上调蛋白83个,下调蛋白97个,表明iTRAQ标记技术结合二维液相色谱串联质谱可有效地分离和鉴定草菇菌丝蛋白质组。该研究结果为更深入全面地研究草菇菌丝蛋白质组学奠定基础。
文摘基于iTRAQ多重标记串联质谱技术系统研究脂多糖刺激下乳腺上皮细胞蛋白的差异表达,并对与乳蛋白、乳脂肪相关差异表达基因进行验证。培养纯化后的乳腺上皮细胞,经脂多糖(LPS)处理后提取细胞蛋白,采用iTRAQ标记和联合二维液相色谱-串联质谱(2D-LC-MS/MS)检测分析得到各组间细胞差异表达蛋白,并采用蛋白印迹和酶联免疫法(ELISA)对差异蛋白进行验证,然后对与乳蛋白、乳脂肪相关基因的相互作用蛋白进行PPI(Protein protein interaction)预测。乳腺上皮细胞共鉴定出2 487个蛋白,其中差异蛋白共341个,与对照组相比,163个蛋白表达上调,178个蛋白表达下调。iTRAQ测定结果显示,LPS处理组与对照组相比,αs1-酪蛋白(CSN1S1)、κ-酪蛋白(CSN3)和脂肪酸合酶(FASN)基因蛋白表达水平有统计学意义;经蛋白印迹试验结果表明,LPS诱导组αs1-酪蛋白表达水平同对照组比较,明显降低(P<0.05);应用ELISA方法测定细胞培养液中αs1-酪蛋白、κ-酪蛋白和脂肪酸合酶的浓度结果显示,LPS诱导组细胞培养液中上述蛋白的浓度明显低于对照组(P<0.05)。综上表明,LPS诱导的炎症反应可影响乳腺上皮细胞的乳蛋白和乳脂肪的合成。
