OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides fromLigustrum robustum(Roxb.) Blume(LRTPG) in hamsters using proteomics technique.METHODS The hamsters were fed with a high fat...OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides fromLigustrum robustum(Roxb.) Blume(LRTPG) in hamsters using proteomics technique.METHODS The hamsters were fed with a high fat diet to induce hyperlipidemia.Then LRTPG of high(1.2 g·kg^(-1)),medium(0.6 g·kg^(-1)) and low(0.3 g·kg^(-1)) doses were administrated daily for 4 weeks.Then the concentrations of plasma and hepatic lipids were determined using enzymic methods.The total protein was extracted from livers of the model group and the group treated with the high dose of LRTPG for label-free quantitative proteomics.RESULTS LRTPG significantly reduced the concentrations of plasma and hepatic lipids in hamsters fed a high fat diet.The proteomics data showed that a total of 2231 proteins were identified,and 549 proteins were found to be differentially expressed between the model group and the group treated with LRTPG.Among the 549 proteins,93 proteins were up-regulated and 59 proteins were down-regulated,and 397 proteins were absent or not.And some of these proteins were much related to the lipid metabolism.Further,gene ontology(GO) analysis indicated metabolic process,transport,oxidation-reduction process,phosphorylation,signal transduction,lipid metabolic process were the main biological processes that those differentially expressed proteins participated.KEGG pathway analysis showed that those proteins were involved in several metabolic pathways including oxidative phosphorylation,non-alcoholic fatty liver disease(NAFLD),PI3K-Akt signaling pathway,cAMP signaling pathway,cGMP-PKG signaling pathway.CONCLUSION The proteomics study could provide valuable clues to help us to understand the hypolipidemic mechanisms of LRTPG much better.展开更多
A comparative proteomic analysis was applied to explore the mechanism of fiber cell development in cotton.Initially,an efficient protein preparation method was established for proteomic analysis
In order to explore the effect of electroacupuncture on rats with acute spinal injury,we established animal model of the spinal injury.Total proteins were extracted from spinal cord of normal rats,acute spinal injury ...In order to explore the effect of electroacupuncture on rats with acute spinal injury,we established animal model of the spinal injury.Total proteins were extracted from spinal cord of normal rats,acute spinal injury rats and acute spinal injury rat treated by electroacupuncture,and separated by 2-DE.10 differential expressed proteins were identified by the MALDI-TOF-TOF-MS with high mass accuracy,high mascot scores and high reliability.展开更多
Proteome means the whole proteins expressed by genome in a cell or tissue.Two- dimensional electrophoresis (2-DE), computer image analysis and mass spectrometry were known as the three key techniques in proteome resea...Proteome means the whole proteins expressed by genome in a cell or tissue.Two- dimensional electrophoresis (2-DE), computer image analysis and mass spectrometry were known as the three key techniques in proteome research. Peptide mass fingerprinting (PMF) is becoming a widely used and rapidly developed technique for protein identification after 2- DE. In this study, a systematic method to identify the proteins after 2-DE by PMF was developed. Proteins were digested in-gel by trypsin and the masses of peptides were measured by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI- TOFMS). the data obtained from PMF were used for protein database searching and protein identification. the proteins from human lung cancer cell isolated by 2-DE were identified by The method developed in this research.展开更多
In order to explore the molecular mechanisms of children adrenal neuroblastoma,and screen biomarkers for early diagnosis of this disease,the comparative proteomics were done in this report.The total proteins in childr...In order to explore the molecular mechanisms of children adrenal neuroblastoma,and screen biomarkers for early diagnosis of this disease,the comparative proteomics were done in this report.The total proteins in children adrenal neuroblastoma and adrenal control tissues were extracted separately and then separated by 2-DE individually.The protein spots were identified eventually by UPLC-HD-MS.In this research,18 difference proteins including stathmin 1 were found.展开更多
Angiopoietin (Ang),as a cytokine found in recent years that can promote angiogenesis,belongs to a growth factor family including Ang 1,Ang 2,Ang 3 and Ang 4.Most research focus on Ang 1 and its receptor Tie 2.Differen...Angiopoietin (Ang),as a cytokine found in recent years that can promote angiogenesis,belongs to a growth factor family including Ang 1,Ang 2,Ang 3 and Ang 4.Most research focus on Ang 1 and its receptor Tie 2.Different from vascular endothelial growth factor,Ang 1/Tie 2 affect the end of angiogenesis,induce cell migration and maintain survive of endothelial cell and play an important role in angiogenesis and maintenance of the stability of the neoformative capillary network.Ang 1 is composed of 498 amino acids.The homology between human and mouse is 96.7%.Ang 1 is extensively distributed in tissues containing rich blood vessels such as muscle,prostate,ovary,uterus,but little is in tissues which have no or a few blood vessel.Adenovirus vector is able to transfect effectively Ang 1 gene to MSC.Previous studies have demonstrated that MSCAng 1 cell can highly express and secrete Ang 1 protein.MSCAng 1 could survive in the cardiac muscle tissue of acute myocardial infarction rat,and express exogenous Ang 1 protein for a period time.In acute myocardial infarction,MSCAng 1 cell have more potent effect on prompting angiogenesis than MSC cell.Moreover,MSCAng 1 cell could further reduce infarct size,increase thickness of cardiac ventricle wall,and improve cardiac muscle reconstitution.This study aim to find differential expressed protein related with Ang 1 using proteomic technologies.Protein spots showing significant difference by gel image analysis and statistics analysis were selected for identification using ESI MS/MS.We hope this work can provide new clues for the study on mechanism of action of Ang 1.展开更多
The differentially expressed proteins between normal and tamoxifen-induced autophagic MCF-7 cells were studied by 2-DE combining with mass spectrometric analysis.Totally,there were 668±99 and 550±97 protein ...The differentially expressed proteins between normal and tamoxifen-induced autophagic MCF-7 cells were studied by 2-DE combining with mass spectrometric analysis.Totally,there were 668±99 and 550±97 protein spots detected in the 2-DE maps from normal and autophagic MCF-7 cells respectively,among which 5 changed protein spots were identified by the Q-TOF MS/MS and database search.展开更多
中国农科院蜜蜂所“蜜蜂蛋白质组学创新团队”继去年解析工蜂胚胎发育分子机理在Molecular＆cellular Proteomics发表后，今年在雄蜂胚胎发育机理方面又取得新的研究进展，研究结果“Proteome analysis unravels mechanism underling th...中国农科院蜜蜂所“蜜蜂蛋白质组学创新团队”继去年解析工蜂胚胎发育分子机理在Molecular＆cellular Proteomics发表后，今年在雄蜂胚胎发育机理方面又取得新的研究进展，研究结果“Proteome analysis unravels mechanism underling the embryogenesis of the honeybee drone and its divergence with the worker（Apismellifera lingustica）”发表在近期的蛋白质组学研究的重要学术期刊上（Journal of Proteome Research）。这也是该团队在本期刊发表的第11篇研究成果。展开更多
Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships betwe...Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships between the genomic variabilities and the current organ-or system-based definition and classification of disease in Western medi⁃cine.The major challenges in the effort to establish and develop precision medicine are how diseases should be defined and classified in an integrated systemic or omic scale and also on an individualized basis.The phenomics approach to the understanding of diseases will allow the transition from focused phenotype/genotype studies to a systemic largescale phenome and genome,proteome,metabolome approach and the identification of a systemically integrated setof biomarkers for diagnosis and prognosis of disease phenome(or Zhenghou).Phenome-wide associated study(PheWAS)may soon lead the field of medical research and provide insightful and novel clues for redefinition of the disease phenome and its clinical classifications and personalized treatment and ultimately precision medicine.Pharma⁃cophenomics is to characterize the phenomes of drug response and also to identify the corresponding therapeutic targets at the level of systems biology.As a complement of pharmacogenomics/proteomics/metabolomics,pharmacoph⁃enomics offers a suite of new technologies and platforms for the transition from focused phenotype-genotype study to a systematic phenome-genome approach and refine drug research with systematically-defined drug response and thera⁃peutic targets.Therefore,pharmacophenomics will provide a new paradigm for the study of drug response including effects and toxicities at the level of systems biology and will identify the corresponding therapeutic targets and principles for combination treatment and prevention of disease using Fangji or Fufang that takes into account individual variability in genes,environment,and lifestyle for each person.展开更多
Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trich...Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.展开更多
Aim Liver fibrosis is a consequence of chronic liver disease which can progress into liver cirrhosis evenhepatocarcinoma. FuzhengHuayu （FZHY） , a Chinese herbal formula, had been reported to have the effect of anti-...Aim Liver fibrosis is a consequence of chronic liver disease which can progress into liver cirrhosis evenhepatocarcinoma. FuzhengHuayu （FZHY） , a Chinese herbal formula, had been reported to have the effect of anti- fibrosis. This study aims to investigate the effective targets and the mechanisms of FZHY on liver fibrosis. Methods The liver tissue samples of normal group, model group and FZHY-treated group were examined by microarray and iTRAQ. Profiles of differentially expressed genes （DEGs） and differentially expressed proteins （DEPs） in CC14-in- duced liver fibrosis model in rat were analyzed. GO and Pathway were analyzed by DAVID, and protein-protein in- teraction （PPI） was analyzed by STRING and cytoscape. The targets of FZHY compounds were predicted by TCM- SP. Results The results showed that 255 genes （ fold change ≥ 1.5, P 〈 0.05） and 507 proteins （ fold change ≥ 1.2 ,P 〈 0.05 ） were differentially expressed between FZHY group and model group. The high-throughput data of transcriptomics and proteomics was analyzed synthetically. DAVID function annotation analysis showed that these DEGS and DEPs both enriched in 15 GO terms, among drug metabolic process, response to extracellular stimulus, response to vitamin, arachidonic acid metabolic process, response to wounding and oxidation reduction may involve in liver fibrosis. KEGG pathway analysis showed that these DEGS and DEPs both enriched in 9 pathways, among arachidonic acid metabolism, retinol metabolism, metabolism of xenobiotics by cytochrome P450 and drug metabo- lism may be related to liver fibrosis. PPI analysis found that 10 overlapped core genes and proteins, among, Ugt2a3, Cyp2bl and Cyp3al8 were of higher degree, which are all enriched in retinol metabolism. Interestedly, Cyp2bl and Cyp3al8 were also predicted with TCMSP as the targets of FZHY compounds. Conclusion The re- sults indicated that the effective mechanism of FZHY against liver fibrosis is involved in the regulation of multiple targets and multiple pathways, among, retinol metabolism pathway by targeting Ugt2a3, Cyp2bl and Cyp3al8 may play an important role in the treatment of liver fibrosis.展开更多
Most drugs exert pharmacological effects through interaction with their target proteins.Therefore,drug target identification is a crucial step towards the understanding of the mechanism of drug action.It is also imper...Most drugs exert pharmacological effects through interaction with their target proteins.Therefore,drug target identification is a crucial step towards the understanding of the mechanism of drug action.It is also imperative to study the pharmacodynamics of a known drug,with an aim to discover the potentially unrevealed actions and thus refine its future clinical applications.Currently,drug-target identification is either through in vitro affinity chromatography-based approaches or in vivo activity-based protein profiling(ABPP)approaches.However,these approaches generally face difficulties discriminating specific drug targets from non-specific ones.To address this issue,we have come up with a strategy by coupling iTRAQTM(isobaric tags for relative and absolute quantitation)quantitative proteomics approach with clickable ABPP,to specifically and compre hensively identify drug targets in live cells.Using this approach,we identified the protein targets of andrographolide,a natural product with known anti-inflammation and anti-cancer effects,in live cancer cells.The identified target list not only confirmed the known functions of the drug but also revealed its potential novel application as a tumor metastasis inhibitor.We have also used this strategy,combining with a cleavable probe to identify the protein targets of aspirin and its binding sites.Our results revealed the roles of aspirin ininhibition of protein synthesis and induction of autophagy,which have been functionally validated.Our strategy is widely applicable to the identification of protein targets of covalent drugs.展开更多
The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample pre...The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.展开更多
In recent years,studies have shown that there is a correlation between sleep disorders and cancer,but at the present stage,the research on sleep disorders and tumor related animal models is relatively insufficient.Our...In recent years,studies have shown that there is a correlation between sleep disorders and cancer,but at the present stage,the research on sleep disorders and tumor related animal models is relatively insufficient.Our research will focus on mice bearing B16F10-luc-G5 melanoma tumor with sleep fragmentation,detecting promoting effect of sleep fragmentation(SF)on the metastasis of melanoma.At the same time,we used Ganoderma lucidum poly⁃saccharides peptide(GL-pp,80 mg·kg-1),a component of traditional Chinese medicine Ganoderma lucidum,which has long enjoyed a good reputation at home and abroad,to observe its anti-tumor metastasis effects on B16F10-luc-G5 mice with SF.Then we used whole proteomics to analyze the difference proteins expressed in lung tissue and compared between groups,includes mice bearing B16F10-luc-G5,mice bearing B16F10-luc-G5 with SF and GL-pp administered mice bearing B16F10-luc-G5 with SF.With the analysis using bioinformatics,we found several key proteins,their genes name are Adcy9,ptk2,Yap1 and Lpin2,Per1 and Tim.And several important clusters,they are,immune system,platelet aggres⁃sion,energy metabolism,cell cytoskeleton,cell adhesion and circadian rhythms.Moreover,we detected the TLR4 signal pathway and macrophage differentiation to reconfirm the results of proteomics and trying to elucidate the mechanism of SF on tumor growth and metastasis and the effects of GL-pp.展开更多
OBJECTIVE Erzhi pills is a clas⁃sic prescription of Chinese medicine originated from Fu Shou Jing Fang in Ming dynasty,with the effects of nourishing kidney-Yin and hemosta⁃sis,black hair,strengthening muscles and bon...OBJECTIVE Erzhi pills is a clas⁃sic prescription of Chinese medicine originated from Fu Shou Jing Fang in Ming dynasty,with the effects of nourishing kidney-Yin and hemosta⁃sis,black hair,strengthening muscles and bones.As a classical prescription for nourishing kidney-Yin,Erzhi pills has been used to treat senile dementia in China for many years.Herein,our study aimed to investigate the protective effects of Erzhi pills in rat models of Alzheimer disease(AD)induced by ovariectomy as well as D-galactose and Aβ1-40 injection and to explore its potential mechanism.METHODS The model of AD rats was established by ovariectomy com⁃bined with D-galactose and Aβ1-40 injection.Ovariectomized rats were randomly divided into four groups:model group,estradiol valerate(0.80 mg·kg-1)group,Erzhi pills high(1.50 mg·kg-1)and low(0.75 mg·kg-1)doses group.In addition,rats of sham operation were selected as the sham operated group.Except for the sham oper⁃ated group,rats were injected intraperitoneally with D-galactose(100 mg·kg-1 per day,for 49 d)on the 8th day,then they were given intracerebro⁃ventricular injection of Aβ1-40(10μg per rat,1 g·L-1)on the 36th day,while the corresponding drugs were given by gastrointestinal administra⁃tion on the 22nd day.In our study,Morris water maze test was used to evaluate the learning and memory abilities,while ELISA kit was used to an⁃alyze serum estrogen level.The morphology of hippocampal neuron cells was observed by HE staining,and Nissl staining was utilized to ob⁃serve the Nissl body in cytoplasm.Then,the ex⁃pression of ERβpositive cells and hippocampal Aβ1-40 and p-Tau404 proteins was determined by immunohistochemistry.In order to further explore the molecular mechanism of Erzhi pills preven⁃tion and treatment of AD,proteomics was used to find potential targets and related pathways,Western blotting was used to verify the expres⁃sion of candidate differential protein.According to the results of proteomics in our experiment,Western blotting was used to detect the protein expression of PI3K,Akt,Bcl-2,Bcl-xl,Bad,14-3-3 and GSK3β.RESULTS The escape latency was significantly shortened,the number of crossing platform was increased,the neuron arrange⁃ment was more orderly and with less nuclear pycnosis in rats of Erzhi pills groups compared to the model group.In rats treated with Erzhi pills,the number of neurons,Nissl bodies,the estro⁃gen levels and ERβpositive cells were increased,while the number of Aβ1-40 and p-Tau404 positive cells was significantly decreased.Proteomics found that there were more than one hundred differentially expressed proteins of rats treated with Erzhi pills,which were involved in 48 signal⁃ing pathways.Among these proteins,five of them were involved in the PI3K/Akt signal path⁃way.As the down-stream protein of PI3K/Akt sig⁃naling pathway,the content of 14-3-3 protein was significantly increased.Western blotting analysis showed that the expression of p-GSK3β/GSK3βand Bad was decreased,while that of p-Akt/Akt,p-PI3K/PI3K,14-3-3,Bcl-xl and Bcl-2 was up-regulated in rats from the Erzhi pills groups compared with the model group.CON⁃CLUSION Erzhi pills can improve estrogen levels,alter proteomics expression of the hippocampus and activate PI3K/Akt pathway in AD rats,reduce Aβaggregation,inhibit the hyperphos⁃phorylation of Tau protein,maintain the morphol⁃ogy of hippocampal neurons and decrease the apoptosis of hippocampal neurons,thereby improving the learning and memory abilities of ovariectomized AD rats induced by D-galactose and Aβ1-40 injection.This study may provide an experimental basis for the clinical treatment of Erzhi pills.展开更多
To investigate the potential effects of Vaccaria segetalis, we employed the proteomic approach on the dairy cow mammary gland epithelial cells （DCMECs）. A total of 35 differentially expressed nuclear proteins were v...To investigate the potential effects of Vaccaria segetalis, we employed the proteomic approach on the dairy cow mammary gland epithelial cells （DCMECs）. A total of 35 differentially expressed nuclear proteins were visualized by 2-DE and silver nitrate staining. Of these, five proteins also displayed significant expression changes upon treatment of the water decoction from Vaccaria segetalis, and such alterations were further confirmed by RT-PCR. Together, at both the mRNA and protein levels, the water decoction from Vaccaria segetalis increased the expression of proteins ethylmalonic encephalopathy 1 （ETHE1）, vesicle amine transport protein 1 homolog （VAT1）, parkinson disease protein 7 homolog （Protein DJ-1）, proteasome subunit alpha type-2 （PSMA2） and SUMO-activating enzyme subunit 1 （SAE1）. This study would enable a better understanding of the molecular mechanisms underlying this water decoction effects at the protein level.展开更多
The situation of global warming imparts negative impacts on crop growth and development.Cotton is the most important fiber crop around the globe.However,frequent drought episodes pose serious threats to cotton product...The situation of global warming imparts negative impacts on crop growth and development.Cotton is the most important fiber crop around the globe.However,frequent drought episodes pose serious threats to cotton production worldwide.Due to the complex genetic structure of drought tolerance,the development of a tolerant cultivar is cumbersome via conventional breeding.Multiple omics techniques have appeared as successful tool for cotton improvement in drought tolerance.Advanced omics-based biotechniques have paved the way for generation of omics data like transcriptomics,genomics,metabolomics and proteomics,which greatly expand the knowledge of cotton response to drought stress.Omics methodologies and have provided ways for the identification of quantitative trait loci(QTLs),gene regulatory networks,and other regulatory pathways against drought stress in cotton.These resources could speed up the discovery and incorporation of drought tolerant traits in the elite genotypes.The genome wide association study(GWAS),gene-editing system CRISPER/Cas9,gene silencing through RNAi are efficient tools to explore the molecular mechanism of drought tolerance and facilitate the identification of mechanisms and candidate genes for the improvement of drought tolerance in cotton.展开更多
基金supported by the PUMC(Peking Union Medical College)Youth Fund(3332015142) National Natural Science Foundation of China(81703746)
文摘OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides fromLigustrum robustum(Roxb.) Blume(LRTPG) in hamsters using proteomics technique.METHODS The hamsters were fed with a high fat diet to induce hyperlipidemia.Then LRTPG of high(1.2 g·kg^(-1)),medium(0.6 g·kg^(-1)) and low(0.3 g·kg^(-1)) doses were administrated daily for 4 weeks.Then the concentrations of plasma and hepatic lipids were determined using enzymic methods.The total protein was extracted from livers of the model group and the group treated with the high dose of LRTPG for label-free quantitative proteomics.RESULTS LRTPG significantly reduced the concentrations of plasma and hepatic lipids in hamsters fed a high fat diet.The proteomics data showed that a total of 2231 proteins were identified,and 549 proteins were found to be differentially expressed between the model group and the group treated with LRTPG.Among the 549 proteins,93 proteins were up-regulated and 59 proteins were down-regulated,and 397 proteins were absent or not.And some of these proteins were much related to the lipid metabolism.Further,gene ontology(GO) analysis indicated metabolic process,transport,oxidation-reduction process,phosphorylation,signal transduction,lipid metabolic process were the main biological processes that those differentially expressed proteins participated.KEGG pathway analysis showed that those proteins were involved in several metabolic pathways including oxidative phosphorylation,non-alcoholic fatty liver disease(NAFLD),PI3K-Akt signaling pathway,cAMP signaling pathway,cGMP-PKG signaling pathway.CONCLUSION The proteomics study could provide valuable clues to help us to understand the hypolipidemic mechanisms of LRTPG much better.
文摘A comparative proteomic analysis was applied to explore the mechanism of fiber cell development in cotton.Initially,an efficient protein preparation method was established for proteomic analysis
文摘In order to explore the effect of electroacupuncture on rats with acute spinal injury,we established animal model of the spinal injury.Total proteins were extracted from spinal cord of normal rats,acute spinal injury rats and acute spinal injury rat treated by electroacupuncture,and separated by 2-DE.10 differential expressed proteins were identified by the MALDI-TOF-TOF-MS with high mass accuracy,high mascot scores and high reliability.
文摘Proteome means the whole proteins expressed by genome in a cell or tissue.Two- dimensional electrophoresis (2-DE), computer image analysis and mass spectrometry were known as the three key techniques in proteome research. Peptide mass fingerprinting (PMF) is becoming a widely used and rapidly developed technique for protein identification after 2- DE. In this study, a systematic method to identify the proteins after 2-DE by PMF was developed. Proteins were digested in-gel by trypsin and the masses of peptides were measured by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI- TOFMS). the data obtained from PMF were used for protein database searching and protein identification. the proteins from human lung cancer cell isolated by 2-DE were identified by The method developed in this research.
文摘In order to explore the molecular mechanisms of children adrenal neuroblastoma,and screen biomarkers for early diagnosis of this disease,the comparative proteomics were done in this report.The total proteins in children adrenal neuroblastoma and adrenal control tissues were extracted separately and then separated by 2-DE individually.The protein spots were identified eventually by UPLC-HD-MS.In this research,18 difference proteins including stathmin 1 were found.
文摘Angiopoietin (Ang),as a cytokine found in recent years that can promote angiogenesis,belongs to a growth factor family including Ang 1,Ang 2,Ang 3 and Ang 4.Most research focus on Ang 1 and its receptor Tie 2.Different from vascular endothelial growth factor,Ang 1/Tie 2 affect the end of angiogenesis,induce cell migration and maintain survive of endothelial cell and play an important role in angiogenesis and maintenance of the stability of the neoformative capillary network.Ang 1 is composed of 498 amino acids.The homology between human and mouse is 96.7%.Ang 1 is extensively distributed in tissues containing rich blood vessels such as muscle,prostate,ovary,uterus,but little is in tissues which have no or a few blood vessel.Adenovirus vector is able to transfect effectively Ang 1 gene to MSC.Previous studies have demonstrated that MSCAng 1 cell can highly express and secrete Ang 1 protein.MSCAng 1 could survive in the cardiac muscle tissue of acute myocardial infarction rat,and express exogenous Ang 1 protein for a period time.In acute myocardial infarction,MSCAng 1 cell have more potent effect on prompting angiogenesis than MSC cell.Moreover,MSCAng 1 cell could further reduce infarct size,increase thickness of cardiac ventricle wall,and improve cardiac muscle reconstitution.This study aim to find differential expressed protein related with Ang 1 using proteomic technologies.Protein spots showing significant difference by gel image analysis and statistics analysis were selected for identification using ESI MS/MS.We hope this work can provide new clues for the study on mechanism of action of Ang 1.
文摘The differentially expressed proteins between normal and tamoxifen-induced autophagic MCF-7 cells were studied by 2-DE combining with mass spectrometric analysis.Totally,there were 668±99 and 550±97 protein spots detected in the 2-DE maps from normal and autophagic MCF-7 cells respectively,among which 5 changed protein spots were identified by the Q-TOF MS/MS and database search.
文摘中国农科院蜜蜂所“蜜蜂蛋白质组学创新团队”继去年解析工蜂胚胎发育分子机理在Molecular＆cellular Proteomics发表后，今年在雄蜂胚胎发育机理方面又取得新的研究进展，研究结果“Proteome analysis unravels mechanism underling the embryogenesis of the honeybee drone and its divergence with the worker（Apismellifera lingustica）”发表在近期的蛋白质组学研究的重要学术期刊上（Journal of Proteome Research）。这也是该团队在本期刊发表的第11篇研究成果。
文摘Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships between the genomic variabilities and the current organ-or system-based definition and classification of disease in Western medi⁃cine.The major challenges in the effort to establish and develop precision medicine are how diseases should be defined and classified in an integrated systemic or omic scale and also on an individualized basis.The phenomics approach to the understanding of diseases will allow the transition from focused phenotype/genotype studies to a systemic largescale phenome and genome,proteome,metabolome approach and the identification of a systemically integrated setof biomarkers for diagnosis and prognosis of disease phenome(or Zhenghou).Phenome-wide associated study(PheWAS)may soon lead the field of medical research and provide insightful and novel clues for redefinition of the disease phenome and its clinical classifications and personalized treatment and ultimately precision medicine.Pharma⁃cophenomics is to characterize the phenomes of drug response and also to identify the corresponding therapeutic targets at the level of systems biology.As a complement of pharmacogenomics/proteomics/metabolomics,pharmacoph⁃enomics offers a suite of new technologies and platforms for the transition from focused phenotype-genotype study to a systematic phenome-genome approach and refine drug research with systematically-defined drug response and thera⁃peutic targets.Therefore,pharmacophenomics will provide a new paradigm for the study of drug response including effects and toxicities at the level of systems biology and will identify the corresponding therapeutic targets and principles for combination treatment and prevention of disease using Fangji or Fufang that takes into account individual variability in genes,environment,and lifestyle for each person.
文摘Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.
文摘Aim Liver fibrosis is a consequence of chronic liver disease which can progress into liver cirrhosis evenhepatocarcinoma. FuzhengHuayu （FZHY） , a Chinese herbal formula, had been reported to have the effect of anti- fibrosis. This study aims to investigate the effective targets and the mechanisms of FZHY on liver fibrosis. Methods The liver tissue samples of normal group, model group and FZHY-treated group were examined by microarray and iTRAQ. Profiles of differentially expressed genes （DEGs） and differentially expressed proteins （DEPs） in CC14-in- duced liver fibrosis model in rat were analyzed. GO and Pathway were analyzed by DAVID, and protein-protein in- teraction （PPI） was analyzed by STRING and cytoscape. The targets of FZHY compounds were predicted by TCM- SP. Results The results showed that 255 genes （ fold change ≥ 1.5, P 〈 0.05） and 507 proteins （ fold change ≥ 1.2 ,P 〈 0.05 ） were differentially expressed between FZHY group and model group. The high-throughput data of transcriptomics and proteomics was analyzed synthetically. DAVID function annotation analysis showed that these DEGS and DEPs both enriched in 15 GO terms, among drug metabolic process, response to extracellular stimulus, response to vitamin, arachidonic acid metabolic process, response to wounding and oxidation reduction may involve in liver fibrosis. KEGG pathway analysis showed that these DEGS and DEPs both enriched in 9 pathways, among arachidonic acid metabolism, retinol metabolism, metabolism of xenobiotics by cytochrome P450 and drug metabo- lism may be related to liver fibrosis. PPI analysis found that 10 overlapped core genes and proteins, among, Ugt2a3, Cyp2bl and Cyp3al8 were of higher degree, which are all enriched in retinol metabolism. Interestedly, Cyp2bl and Cyp3al8 were also predicted with TCMSP as the targets of FZHY compounds. Conclusion The re- sults indicated that the effective mechanism of FZHY against liver fibrosis is involved in the regulation of multiple targets and multiple pathways, among, retinol metabolism pathway by targeting Ugt2a3, Cyp2bl and Cyp3al8 may play an important role in the treatment of liver fibrosis.
文摘Most drugs exert pharmacological effects through interaction with their target proteins.Therefore,drug target identification is a crucial step towards the understanding of the mechanism of drug action.It is also imperative to study the pharmacodynamics of a known drug,with an aim to discover the potentially unrevealed actions and thus refine its future clinical applications.Currently,drug-target identification is either through in vitro affinity chromatography-based approaches or in vivo activity-based protein profiling(ABPP)approaches.However,these approaches generally face difficulties discriminating specific drug targets from non-specific ones.To address this issue,we have come up with a strategy by coupling iTRAQTM(isobaric tags for relative and absolute quantitation)quantitative proteomics approach with clickable ABPP,to specifically and compre hensively identify drug targets in live cells.Using this approach,we identified the protein targets of andrographolide,a natural product with known anti-inflammation and anti-cancer effects,in live cancer cells.The identified target list not only confirmed the known functions of the drug but also revealed its potential novel application as a tumor metastasis inhibitor.We have also used this strategy,combining with a cleavable probe to identify the protein targets of aspirin and its binding sites.Our results revealed the roles of aspirin ininhibition of protein synthesis and induction of autophagy,which have been functionally validated.Our strategy is widely applicable to the identification of protein targets of covalent drugs.
文摘The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.
文摘In recent years,studies have shown that there is a correlation between sleep disorders and cancer,but at the present stage,the research on sleep disorders and tumor related animal models is relatively insufficient.Our research will focus on mice bearing B16F10-luc-G5 melanoma tumor with sleep fragmentation,detecting promoting effect of sleep fragmentation(SF)on the metastasis of melanoma.At the same time,we used Ganoderma lucidum poly⁃saccharides peptide(GL-pp,80 mg·kg-1),a component of traditional Chinese medicine Ganoderma lucidum,which has long enjoyed a good reputation at home and abroad,to observe its anti-tumor metastasis effects on B16F10-luc-G5 mice with SF.Then we used whole proteomics to analyze the difference proteins expressed in lung tissue and compared between groups,includes mice bearing B16F10-luc-G5,mice bearing B16F10-luc-G5 with SF and GL-pp administered mice bearing B16F10-luc-G5 with SF.With the analysis using bioinformatics,we found several key proteins,their genes name are Adcy9,ptk2,Yap1 and Lpin2,Per1 and Tim.And several important clusters,they are,immune system,platelet aggres⁃sion,energy metabolism,cell cytoskeleton,cell adhesion and circadian rhythms.Moreover,we detected the TLR4 signal pathway and macrophage differentiation to reconfirm the results of proteomics and trying to elucidate the mechanism of SF on tumor growth and metastasis and the effects of GL-pp.
文摘OBJECTIVE Erzhi pills is a clas⁃sic prescription of Chinese medicine originated from Fu Shou Jing Fang in Ming dynasty,with the effects of nourishing kidney-Yin and hemosta⁃sis,black hair,strengthening muscles and bones.As a classical prescription for nourishing kidney-Yin,Erzhi pills has been used to treat senile dementia in China for many years.Herein,our study aimed to investigate the protective effects of Erzhi pills in rat models of Alzheimer disease(AD)induced by ovariectomy as well as D-galactose and Aβ1-40 injection and to explore its potential mechanism.METHODS The model of AD rats was established by ovariectomy com⁃bined with D-galactose and Aβ1-40 injection.Ovariectomized rats were randomly divided into four groups:model group,estradiol valerate(0.80 mg·kg-1)group,Erzhi pills high(1.50 mg·kg-1)and low(0.75 mg·kg-1)doses group.In addition,rats of sham operation were selected as the sham operated group.Except for the sham oper⁃ated group,rats were injected intraperitoneally with D-galactose(100 mg·kg-1 per day,for 49 d)on the 8th day,then they were given intracerebro⁃ventricular injection of Aβ1-40(10μg per rat,1 g·L-1)on the 36th day,while the corresponding drugs were given by gastrointestinal administra⁃tion on the 22nd day.In our study,Morris water maze test was used to evaluate the learning and memory abilities,while ELISA kit was used to an⁃alyze serum estrogen level.The morphology of hippocampal neuron cells was observed by HE staining,and Nissl staining was utilized to ob⁃serve the Nissl body in cytoplasm.Then,the ex⁃pression of ERβpositive cells and hippocampal Aβ1-40 and p-Tau404 proteins was determined by immunohistochemistry.In order to further explore the molecular mechanism of Erzhi pills preven⁃tion and treatment of AD,proteomics was used to find potential targets and related pathways,Western blotting was used to verify the expres⁃sion of candidate differential protein.According to the results of proteomics in our experiment,Western blotting was used to detect the protein expression of PI3K,Akt,Bcl-2,Bcl-xl,Bad,14-3-3 and GSK3β.RESULTS The escape latency was significantly shortened,the number of crossing platform was increased,the neuron arrange⁃ment was more orderly and with less nuclear pycnosis in rats of Erzhi pills groups compared to the model group.In rats treated with Erzhi pills,the number of neurons,Nissl bodies,the estro⁃gen levels and ERβpositive cells were increased,while the number of Aβ1-40 and p-Tau404 positive cells was significantly decreased.Proteomics found that there were more than one hundred differentially expressed proteins of rats treated with Erzhi pills,which were involved in 48 signal⁃ing pathways.Among these proteins,five of them were involved in the PI3K/Akt signal path⁃way.As the down-stream protein of PI3K/Akt sig⁃naling pathway,the content of 14-3-3 protein was significantly increased.Western blotting analysis showed that the expression of p-GSK3β/GSK3βand Bad was decreased,while that of p-Akt/Akt,p-PI3K/PI3K,14-3-3,Bcl-xl and Bcl-2 was up-regulated in rats from the Erzhi pills groups compared with the model group.CON⁃CLUSION Erzhi pills can improve estrogen levels,alter proteomics expression of the hippocampus and activate PI3K/Akt pathway in AD rats,reduce Aβaggregation,inhibit the hyperphos⁃phorylation of Tau protein,maintain the morphol⁃ogy of hippocampal neurons and decrease the apoptosis of hippocampal neurons,thereby improving the learning and memory abilities of ovariectomized AD rats induced by D-galactose and Aβ1-40 injection.This study may provide an experimental basis for the clinical treatment of Erzhi pills.
基金Supported by Major State Basic Research Development Program of China (973 Program, 2011CB100804)
文摘To investigate the potential effects of Vaccaria segetalis, we employed the proteomic approach on the dairy cow mammary gland epithelial cells （DCMECs）. A total of 35 differentially expressed nuclear proteins were visualized by 2-DE and silver nitrate staining. Of these, five proteins also displayed significant expression changes upon treatment of the water decoction from Vaccaria segetalis, and such alterations were further confirmed by RT-PCR. Together, at both the mRNA and protein levels, the water decoction from Vaccaria segetalis increased the expression of proteins ethylmalonic encephalopathy 1 （ETHE1）, vesicle amine transport protein 1 homolog （VAT1）, parkinson disease protein 7 homolog （Protein DJ-1）, proteasome subunit alpha type-2 （PSMA2） and SUMO-activating enzyme subunit 1 （SAE1）. This study would enable a better understanding of the molecular mechanisms underlying this water decoction effects at the protein level.
文摘The situation of global warming imparts negative impacts on crop growth and development.Cotton is the most important fiber crop around the globe.However,frequent drought episodes pose serious threats to cotton production worldwide.Due to the complex genetic structure of drought tolerance,the development of a tolerant cultivar is cumbersome via conventional breeding.Multiple omics techniques have appeared as successful tool for cotton improvement in drought tolerance.Advanced omics-based biotechniques have paved the way for generation of omics data like transcriptomics,genomics,metabolomics and proteomics,which greatly expand the knowledge of cotton response to drought stress.Omics methodologies and have provided ways for the identification of quantitative trait loci(QTLs),gene regulatory networks,and other regulatory pathways against drought stress in cotton.These resources could speed up the discovery and incorporation of drought tolerant traits in the elite genotypes.The genome wide association study(GWAS),gene-editing system CRISPER/Cas9,gene silencing through RNAi are efficient tools to explore the molecular mechanism of drought tolerance and facilitate the identification of mechanisms and candidate genes for the improvement of drought tolerance in cotton.
