Objective:To screen potential serum differential proteins in insulin resistance(IR)complicated with polycystic ovary syndrome(PCOS)using isobaric tags for relative and absolute quantitation(i TRAQ)combined with ultra-...Objective:To screen potential serum differential proteins in insulin resistance(IR)complicated with polycystic ovary syndrome(PCOS)using isobaric tags for relative and absolute quantitation(i TRAQ)combined with ultra-high performance liquid chromatography-tandem mass spectrometry(LC-MS/MS).Methods:A total of 20 patients diagnosed with PCOS in our hospital were selected,including 10 cases of simple PCOS and 10 cases of PCOS+IR.i TRAQ combined with LC-MS/MS was used for proteomic analysis to identify serum differential proteins.Bioinformatics analyses,including gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and protein-protein interaction(PPI)analysis,were conducted to understand the biological processes,cellular components,and molecular functions of the differentially expressed proteins detected by the two methods.Results:A total of 454,675 secondary spectra were detected by iTRAQ,with 14,376 matched spectra.Combined with LC-MS/MS,74,386peptides,47,542 unique peptide sequences,and 54,675 proteins were identified.A total of 249 differentially expressed proteins with a fold change≥1.30 or≤0.83 were found,among which 9 had a P-value<0.05.There were 5 up-regulated and 4 down-regulated proteins,namely RPAP3,ALDH6A1,COX20,RASSF3,ALPK2,NANOS1,FAM210A,CHGA,and CGA.These differential proteins were imported into the STRING database for PPI network analysis,which revealed 21 nodes and 69 edges with a PPI enrichment P-value<0.001.KEGG enrichment results included hsa04913(Ovarian steroidogenesis),hsa04024(cAMP signaling pathway),and hsa04080(Neuroactive ligand-receptor interaction).Conclusion:The combination of i TRAQ and LC-MS/MS technologies identified nine differential proteins including CHGA and CGA,which are mainly enriched in pathways related to ovarian steroidogenesis,c AMP signaling,and neuroactive ligand-receptor interaction.This combination provides a powerful platform for exploring the pathogenesis of IR complicated with PCOS and discovering new biomarkers.展开更多
The mechanisms of mushroom polysaccharides on immune functions and lipid metabolism of aged mammals have not been fully elucidated.In the present study,after assessing the impacts of one type of Lentinula edodes-deriv...The mechanisms of mushroom polysaccharides on immune functions and lipid metabolism of aged mammals have not been fully elucidated.In the present study,after assessing the impacts of one type of Lentinula edodes-derived polysaccharides,named L2,on immune functions and blood lipid profiles,isobaric tags for relative and absolute quantification(iTRAQ)-based proteomic profiling of the small intestinal tissues from aged mice treated with L2 was performed.L2 reversed immune function declines and modulated the lipid metabolism of aged mice evidenced by increased levels of serum TC,HDL-C,and LDL-C,and reduced levels of serum TG.Moreover,a total of 95 differentially regulated proteins(DRPs) were identified,of which75 were up-regulated and 20 were down-regulated.Most of the DRPs were involved in intracellular and extracellular structure organization,and cellular and metabolic regulation.Particularly,approximately 16 and 9 DRPs participated in the regulation of immune functions and lipid metabolism,respectively.Furthermore,protein-protein interaction analysis highlighted that cadherin-1,plectin,cadherin-17,Ras GTPase-activating-like protein IQGAP2,and ezrin might be key proteins in response to L2 treatment.These findings provide new insights into the biological mechanisms of mushroom polysaccharides in anti-aging from a proteomic perspective.展开更多
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】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
文摘Objective:To screen potential serum differential proteins in insulin resistance(IR)complicated with polycystic ovary syndrome(PCOS)using isobaric tags for relative and absolute quantitation(i TRAQ)combined with ultra-high performance liquid chromatography-tandem mass spectrometry(LC-MS/MS).Methods:A total of 20 patients diagnosed with PCOS in our hospital were selected,including 10 cases of simple PCOS and 10 cases of PCOS+IR.i TRAQ combined with LC-MS/MS was used for proteomic analysis to identify serum differential proteins.Bioinformatics analyses,including gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and protein-protein interaction(PPI)analysis,were conducted to understand the biological processes,cellular components,and molecular functions of the differentially expressed proteins detected by the two methods.Results:A total of 454,675 secondary spectra were detected by iTRAQ,with 14,376 matched spectra.Combined with LC-MS/MS,74,386peptides,47,542 unique peptide sequences,and 54,675 proteins were identified.A total of 249 differentially expressed proteins with a fold change≥1.30 or≤0.83 were found,among which 9 had a P-value<0.05.There were 5 up-regulated and 4 down-regulated proteins,namely RPAP3,ALDH6A1,COX20,RASSF3,ALPK2,NANOS1,FAM210A,CHGA,and CGA.These differential proteins were imported into the STRING database for PPI network analysis,which revealed 21 nodes and 69 edges with a PPI enrichment P-value<0.001.KEGG enrichment results included hsa04913(Ovarian steroidogenesis),hsa04024(cAMP signaling pathway),and hsa04080(Neuroactive ligand-receptor interaction).Conclusion:The combination of i TRAQ and LC-MS/MS technologies identified nine differential proteins including CHGA and CGA,which are mainly enriched in pathways related to ovarian steroidogenesis,c AMP signaling,and neuroactive ligand-receptor interaction.This combination provides a powerful platform for exploring the pathogenesis of IR complicated with PCOS and discovering new biomarkers.
基金supported by the Key-Area Research and Development Program of Guangdong Province (2021B0707060001)the Program for Scientific Research Start-Up Funds of Guangdong Ocean UniversityChina Postdoctoral Science Foundation (2016T90787)。
文摘The mechanisms of mushroom polysaccharides on immune functions and lipid metabolism of aged mammals have not been fully elucidated.In the present study,after assessing the impacts of one type of Lentinula edodes-derived polysaccharides,named L2,on immune functions and blood lipid profiles,isobaric tags for relative and absolute quantification(iTRAQ)-based proteomic profiling of the small intestinal tissues from aged mice treated with L2 was performed.L2 reversed immune function declines and modulated the lipid metabolism of aged mice evidenced by increased levels of serum TC,HDL-C,and LDL-C,and reduced levels of serum TG.Moreover,a total of 95 differentially regulated proteins(DRPs) were identified,of which75 were up-regulated and 20 were down-regulated.Most of the DRPs were involved in intracellular and extracellular structure organization,and cellular and metabolic regulation.Particularly,approximately 16 and 9 DRPs participated in the regulation of immune functions and lipid metabolism,respectively.Furthermore,protein-protein interaction analysis highlighted that cadherin-1,plectin,cadherin-17,Ras GTPase-activating-like protein IQGAP2,and ezrin might be key proteins in response to L2 treatment.These findings provide new insights into the biological mechanisms of mushroom polysaccharides in anti-aging from a proteomic perspective.
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】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。
