Sini Decoction (SNT) is a traditional formula recognized for its efficacy in warming the spleen and stomach and dispersing cold. However, elucidating the mechanism of action of SNT remains challenging due to its complex multiple components. This study utilized a synergistic approach combining two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE)-based drug affinity responsive target stability (DARTS) with label-free quantitative proteomics techniques to identify the direct and indirect protein targets of SNT in myocardial infarction. The analysis identified 590 proteins, with 30 proteins showing significant upregulation and 51 proteins showing downregulation when comparing the SNT group with the model group. Through the integration of 2D-DIGE DARTS with proteomics data and pharmacological assessments, the findings indicate that protein disulfide-isomerase A3 (PDIA3) may serve as a potential protein target through which SNT provides protective effects on myocardial cells during myocardial infarction.
Myocardial Infarction/genetics* ; Proteomics/methods* ; Drugs, Chinese Herbal/chemistry* ; Animals ; Protein Disulfide-Isomerases/genetics* ; Male ; Two-Dimensional Difference Gel Electrophoresis/methods* ; Humans ; Rats ; Rats, Sprague-Dawley ; Electrophoresis, Gel, Two-Dimensional

In this study,the protein in different Cordyceps samples,which include fresh sample( S1),22 ℃ drying sample( S2),37 ℃ drying sample( S3) and 60 ℃ drying sample( S4),were analyzed by sodium dodecylsupinate-polyacrylamide gel electrophoresis( SDS-PAGE) and two-dimensional electrophoresis( 2-DE). The total protein contents in Cordyceps samples were from 1. 655-4. 493 mg·g~(-1) and the protein contents in fresh sample was the highest. The results of SDS-PAGE showed that the mainly ranges of protein molecular weight of Cordyces samples were 10-100 kDa and the numbers of protein bands were 28 to 41,the fresh sample had the maximum number of protein bands. The 2-DE profiles were analyzed by PDQuest software. The resulted indicated that 488-876 protein spots were detected in different Cordyceps samples and the isoelectric point( pI) was distributed between 4. 5 and 6. 5,the protein molecular weight was distributed in 10-20 kDa and 25-100 kDa,the fresh sample had the maximum number of protein spots. Therefore,the drying process could decrease contents and species of protein in Cordyceps,and the different drying conditions had different effects on protein. These results provide a reference for improving the drying process of Cordyceps.
Cordyceps ; chemistry ; Desiccation ; methods ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Fungal Proteins ; analysis ; Molecular Weight

Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image.
Algorithms ; Animals ; Electrophoresis, Gel, Two-Dimensional ; methods ; Humans ; Image Processing, Computer-Assisted ; methods ; Proteins ; analysis ; Proteomics ; methods ; Software

OBJECTIVE: To investigate the innate characters of 3 endometriosis (EMT) syndromes, blood stasis (BS), qi stagnation and blood stasis (QSBS) as well as Shen (Kidney) deficiency and blood stasis (KDBS) in terms of proteomics, lay a molecular biological basis for the differentiation of various blood stasis syndromes of EMT, establish a EMT microscopic syndrome differentiation and diagnosis system in terms of proteomics, discover the evolution principles and therapeutic targets of these EMT syndromes, and search their signifificant molecular markers and genetic intervention targets. METHODS: Six specimens from the ectopic and entopic endometrium tissues of patients with EMT in each syndrome, BS, QSBS as well as KDBS, in the early proliferative phase of the menstrual cycle, and 6 specimens from normal endometrium tissues in the early proliferative phase of the menstrual cycle were obtained. Three groups were formed in each syndrome by mixing two random specimens in equal amount, and then their respective two-dimensional electrophoresis graphs were obtained after total protein extraction. Finally, the detected differences in protein expression were identifified through matrix-assisted laser desorption Ionization-time of flflight mass spectrometry (MALDI-TOF/MS) and protein database. RESULTS: The results of differential proteins expressed in each syndrome were shown as follows: BS syndrome had 2 differential proteins in entopic endometrium and 1 differential protein in ectopic endometrium; KDBS syndrome had 3 in entopic endometrium and 3 in ectopic endometrium; and QSBS syndrome had 3 in entopic endometrium and 4 in ectopic endometrium. It was found out that annexin was highly expressed in both entopic and ectopic endometrium of KDBS syndrome; and myosin light chain 3 was highly expressed in both entopic and ectopic endometrium of QSBS syndrome. CONCLUSION There are differential protein expressions among the 3 EMT syndromes, which might be the inner origin of syndrome characters, and these differential proteins might be the candidate biomarkers for the pathogenesis of various EMT syndromes.
Adult ; Electrophoresis, Gel, Two-Dimensional ; Endometriosis ; blood ; metabolism ; Female ; Humans ; Mass Spectrometry ; Proteome ; metabolism ; Proteomics ; methods ; Syndrome

BACKGROUND/AIMS: Acute exacerbations in chronic obstructive pulmonary disease may be related to air pollution, of which ozone is an important constituent. In this study, we investigated the protein profiles associated with ozone-induced exacerbations in a smoking-induced emphysema model. METHODS: Mice were divided into the following groups: group I, no smoking and no ozone (NS + NO); group II, no smoking and ozone (NS + O); group III, smoking and no ozone (S + NO); and group IV, smoking and ozone (S + O). Bronchoalveolar lavage, the mean linear intercept (MLI) on hematoxylin and eosin staining, nano-liquid chromatography-tandem mass spectrometry (LC-MS/MS), and Western blotting analyses were performed. RESULTS: The MLIs of groups III (S + NO) and IV (S + O) (45 +/- 2 and 44 +/- 3 microm, respectively) were significantly higher than those of groups I (NS + NO) and II (NS + O) (26 +/- 2 and 23 +/- 2 microm, respectively; p < 0.05). Fourteen spots that showed significantly different intensities on image analyses of two-dimensional (2D) protein electrophoresis in group I (NS + NO) were identified by LC-MS/MS. The levels of six proteins were higher in group IV (S + O). The levels of vimentin, lactate dehydrogenase A, and triose phosphate isomerase were decreased by both smoking and ozone treatment in Western blotting and proteomic analyses. In contrast, TBC1 domain family 5 (TBC1D5) and lamin A were increased by both smoking and ozone treatment. CONCLUSIONS: TBC1D5 could be a biomarker of ozone-induced lung injury in emphysema.
Animals ; Biological Markers/metabolism ; Blotting, Western ; Bronchoalveolar Lavage Fluid/chemistry/cytology ; Chromatography, Liquid ; Disease Models, Animal ; Electrophoresis, Gel, Two-Dimensional ; Lung/*metabolism/pathology ; Male ; Mice, Inbred C57BL ; *Ozone ; Proteins/*metabolism ; *Proteomics/methods ; Pulmonary Disease, Chronic Obstructive/etiology/*metabolism/pathology ; Pulmonary Emphysema/etiology/*metabolism/pathology ; Smoking/*adverse effects ; Tandem Mass Spectrometry

OBJECTIVETo study the dynamic changes in the protein marker expression in the spermatogonial stem cells (SSCs) of mice at different ages by iTRAQ protein mass spectrometry and to screen new markers using the bioinformatic proteome database.

METHODSBased on the postnatal weeks, we divided 80 healthy male C57BL/6 mice into eight age groups of equal number, harvested their testicular tissues, extracted proteins following purification of the SSCs by compound enzyme digestion and magnetic-activated cell sorting. Then we analyzed and identified proteins using two-dimensional electrophoresis, protein mass spectrometry, and protein database information.

RESULTSTotally, 248,510 mass spectra were obtained from the MS experiment and 1132 proteins were identified. By the criteria of >1.2-fold for protein abundance difference and P value <0.05, we identified 298 differentially expressed proteins and 9 currently known makers of SSCs (PCNA, GFRalpha1, CDH1, Annexin A7, UCHL1, VASA, CD49f, CD29, and PLZf). Compara- tive analysis showed different expressions of the proteins in the SSCs of the mice of different ages, and the differences in the expressions of GFRalpha1, CD49f, and CD29 were consistent with the findings in other published literature. Ten proteins (P63, CD71, CD98, K19, ACE, K18, K15, K17, SH2, and SH3) were selected as SSC markers to be further studied.

CONCLUSIONThe proteins in SSCs are differentially expressed in mice of different ages. The technology of iTRAQ protein mass spectrometry can be used to analyze and compare the proteome information of mouse SSCs, obtain differentially expressed proteins in mice of different ages, and thus offers a new ap- proach to further analysis and study of the function and roles of these differential proteins.

Adult Stem Cells ; cytology ; metabolism ; Age Factors ; Animals ; Biomarkers ; analysis ; metabolism ; Cell Separation ; methods ; Electrophoresis, Gel, Two-Dimensional ; Male ; Mass Spectrometry ; Mice ; Mice, Inbred C57BL ; Proteins ; analysis ; metabolism ; Spermatogonia ; cytology

PURPOSE: Recent evidence shows that nitric oxide (NO) may exhibit both pro-cancer and anti-cancer activities. The present study aimed to determine the differentially expressed proteins in NO-treated NIH/3T3 fibroblasts in order to investigate whether NO induces proteins with pro-cancer or anti-cancer effects. MATERIALS AND METHODS: The cells were treated with 300 microM of an NO donor 3,3-bis-(aminoethyl)-1-hydroxy-2-oxo-1-triazene (NOC-18) for 12 h. The changed protein patterns, which were separated by two-dimensional electrophoresis using pH gradients of 4-7, were conclusively identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of the peptide digests. RESULTS: Seventeen differentially expressed proteins were identified in NOC-18-treated cells. Nine proteins [vinculin protein, keratin 19, ubiquitous tropomodulin, F-actin capping protein (alpha1 subunit), tropomyosin 3, 26S proteasome-associated pad1 homolog, T-complex protein 1 (epsilon subunit) N(G)-dimethylarginine dimethylaminohydrolase, and heat shock protein 90] were increased and eight proteins (heat shock protein 70, glucosidase II, lamin B1, calreticulin, nucleophosmin 1, microtubule-associated protein retinitis pigmentosa/end binding family member 1, 150 kD oxygen-regulated protein precursor, and heat shock 70-related protein albino or pale green 2) were decreased by NOC-18 in the cells. Thirteen proteins are related to the suppression of cancer cell proliferation, invasion, and metastasis while two proteins (heat shock protein 90 and N(G)-dimethylarginine dimethylaminohydrolase) are related to carcinogenesis. The functions of 150 kD oxygen-regulated protein precursor and T-complex protein 1 (epsilon subunit) are unknown in relation to carcinogenesis. CONCLUSION: Most proteins differentially expressed by NOC-18 are involved in inhibiting cancer development.
Animals ; Electrophoresis, Gel, Two-Dimensional/*methods ; Fibroblasts/*metabolism/pathology ; HSP70 Heat-Shock Proteins ; Humans ; Mice ; NIH 3T3 Cells ; Neoplasms/*metabolism/pathology ; Nitric Oxide Donors ; Nitroso Compounds ; Proteins/analysis/*metabolism ; Proteomics/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

OBJECTIVETo analyze the differences in serum proteomic profiles between patients with silicosis and chronic bronchitis and to investigate the pathogenesis, clinical diagnosis, and treatment of these two disease.

METHODSSerum samples from patients with stage I silicosis and chronic bronchitis were collected. Two-dimensional gel electrophoresis was performed and protein plots with expression differences higher than 2-fold were identified and further analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

RESULTSCompared with the silicosis group, the chronic bronchitis group had 11 up-regulated proteins and 23 down-regulated proteins. The chronic bronchitis group had high expression of proteins such as interferon beta precursor, apolipoprotein precursor, and transforming growth factor beta1 precursor. The silicosis group had high expression of proteins such as interleukin-6, granzyme A, cathepsin G, and glycoprotein precursor.

CONCLUSIONThe differentially expressed proteins are mainly involved in the activity of serine enzymes, cytotoxicity, inflammation response, and apolipoprotein transfer and play different roles in silicosis and chronic bronchitis.

Bronchitis, Chronic ; pathology ; Cathepsin G ; Down-Regulation ; Electrophoresis, Gel, Two-Dimensional ; Glycoproteins ; Granzymes ; Humans ; Interleukin-6 ; Mass Spectrometry ; Proteomics ; methods ; Serum ; chemistry ; Silicosis ; pathology ; Up-Regulation

OBJECTIVETo explore the abnormal expression of plasma proteins by analysis of proteomic expression profile in children with infectious mononucleosis (IM).

METHODSTwo dimensional gel electrophoresis (2-DE) followed by the mass spectrometry was used to examine important protein spots with different expression levels between children with IM and normal controls.

RESULTSSeven differential proteins were obtained: hemopexin, vitamin D binding protein, fetuin A, C-reactive protein, apolipoprotein A, haptoglobin and transthyretin. Compared with the control group, haptoglobin showed a higher expression level in children with IM, and the expression levels of the other proteins were obviously down-regulated.

CONCLUSIONSThe expression changes of differential proteins identified in this study are all related with the liver acute injury, suggesting that children with IM are associated with acute liver injury. Further studies on the characteristics of above proteins will contribute to the diagnosis and treatment of pediatric IM.

Blood Proteins ; analysis ; Child ; Child, Preschool ; Electrophoresis, Gel, Two-Dimensional ; Female ; Humans ; Infectious Mononucleosis ; blood ; Male ; Proteomics ; methods

Gambogic acid (GA) is an anticancer agent in phase ‖b clinical trial in China but its mechanism of action has not been fully clarified. The present study was designed to search the possible target-related proteins of GA in cancer cells using proteomic method and establish possible network using bioinformatic analysis. Cytotoxicity and anti-migration effects of GA in MDA-MB-231 cells were checked using MTT assay, flow cytometry, wound migration assay, and chamber migration assay. Possible target-related proteins of GA at early (3 h) and late stage (24 h) of treatment were searched using a proteomic technology, two-dimensional electrophoresis (2-DE). The possible network of GA was established using bioinformatic analysis. The intracellular expression levels of vimentin, keratin 18, and calumenin were determined using Western blotting. GA inhibited cell proliferation and induced cell cycle arrest at G2/M phase and apoptosis in MDA-MB-231 cells. Additionally, GA exhibited anti-migration effects at non-toxic doses. In 2-DE analysis, totally 23 possible GA targeted proteins were found, including those with functions in cytoskeleton and transport, regulation of redox state, metabolism, ubiquitin-proteasome system, transcription and translation, protein transport and modification, and cytokine. Network analysis of these proteins suggested that cytoskeleton-related proteins might play important roles in the effects of GA. Results of Western blotting confirmed the cleavage of vimentin, increase in keratin 18, and decrease in calumenin levels in GA-treated cells. In summary, GA is a multi-target compound and its anti-cancer effects may be based on several target-related proteins such as cytoskeleton-related proteins.
Antineoplastic Agents ; pharmacokinetics ; Apoptosis ; drug effects ; Breast Neoplasms ; drug therapy ; metabolism ; Calcium-Binding Proteins ; genetics ; Cell Line, Tumor ; Cell Migration Assays ; Cell Migration Inhibition ; drug effects ; Cell Proliferation ; drug effects ; Computational Biology ; methods ; Cytoskeleton ; metabolism ; Electrophoresis, Gel, Two-Dimensional ; Flow Cytometry ; Gene Expression ; Humans ; Keratin-18 ; genetics ; Oxidation-Reduction ; Protein Biosynthesis ; drug effects ; Protein Transport ; Proteomics ; methods ; Transcription, Genetic ; drug effects ; Ubiquitin-Specific Proteases ; pharmacokinetics ; Vimentin ; genetics ; Xanthones ; pharmacokinetics