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Comparative proteomic analysis of drug sodium iron chlorophyllin addition to Hep 3B cell line.
Zhang, J, Wang, W, Yang, F, Zhou, X, Jin, H, Yang, PY
The Analyst. 2012;(18):4287-94
Abstract
The human hepatoma 3B cell line was chosen as an experimental model for in vitro test of drug screening. The drugs included chlorophyllin and its derivatives such as fluo-chlorophyllin, sodium copper chlorophyllin, and sodium iron chlorophyllin. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) method was used in this study to obtain the primary screening results. The results showed that sodium iron chlorophyllin had the best LC(50) value. Proteomic analysis was then performed for further investigation of the effect of sodium iron chlorophyllin addition to the Hep 3B cell line. The proteins identified from a total protein extract of Hep 3B before and after the drug addition were compared by two-dimensional-gel-electrophoresis. Then 32 three-fold differentially expressed proteins were successfully identified by MALDI-TOF-TOF-MS. There are 29 unique proteins among those identified proteins. These proteins include proliferating cell nuclear antigen (PCNA), T-complex protein, heterogeneous nuclear protein, nucleophosmin, heat shock protein A5 (HspA5) and peroxiredoxin. HspA5 is one of the proteins which are involved in protecting cancer cells against stress-induced apoptosis in cultured cells, protecting them against apoptosis through various mechanisms. Peroxiredoxin has anti-oxidant function and is related to cell proliferation, and signal transduction. It can protect the oxidation of other proteins. Peroxiredoxin has a close relationship with cancer and can eventually become a disease biomarker. This might help to develop a novel treatment method for carcinoma cancer.
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2.
Common variant (rs9939609) in the FTO gene is associated with metabolic syndrome.
Zhou, D, Liu, H, Zhou, M, Wang, S, Zhang, J, Liao, L, He, F
Molecular biology reports. 2012;(6):6555-61
Abstract
Recent genome-wide association studies have showed that common variant (rs9939609) in fat mass and obesity associated (FTO) gene was significantly associated with type 2 diabetes through an effect on human body mass index/obesity. Further studies have suggested that this variant was also involved in the development of metabolic syndrome (MetS). However, the results have been inconsistent. In this study, we performed a meta-analysis to clarify the association between rs9939609 polymorphism and the risk of MetS. Published literature from PubMed, EMBASE and other databases were searched. All studies assessing the association between rs9939609 polymorphism and the risk of MetS were identified. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed-effects model. Thirteen studies (8,370 cases and 23,156 controls) using NCEP ATPIII criteria for MetS were pooled with a meta-analysis. The overall result showed that there was a statistically significant association between rs9939609 polymorphism and MetS risk (OR = 1.11, 95% CI = 1.06-1.17). Subgroup analysis based on ethnicity showed that effect size was only statistically significant in Europeans (OR = 1.11, 95% CI = 1.05-1.16). Eight studies (1,256 cases and 2,551 controls) using IDF criteria for MetS were pooled with a meta-analysis. The overall analysis suggested that rs9939609 polymorphism was significantly associated with MetS risk (OR = 1.32, 95% CI = 1.13-1.54). Subgroup analysis stratified by ethnicity suggested that effect size was only statistically significant in Asians (OR = 1.33, 95% CI = 1.10-1.61). Our results suggested that FTO rs9939609 polymorphism was significantly associated with the increased risk of MetS in European and Asian populations. Mechanistic investigation is also needed to clarify the effect of FTO gene in the predisposition to MetS.
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3.
Protein-centric data integration for functional analysis of comparative proteomics data.
McGarvey, PB, Zhang, J, Natale, DA, Wu, CH, Huang, H
Methods in molecular biology (Clifton, N.J.). 2011;:323-39
Abstract
High-throughput proteomic, microarray, protein interaction and other experimental methods all generate long lists of proteins and/or genes that have been identified or have varied in accumulation under the experimental conditions studied. These lists can be difficult to sort through for Biologists to make sense of. Here we describe a next step in data analysis--a bottom-up approach at data integration--starting with protein sequence identifications, mapping them to a common representation of the protein and then bringing in a wide variety of structural, functional, genetic, and disease information related to proteins derived from annotated knowledge bases and then using this information to categorize the lists using Gene Ontology (GO) terms and mappings to biological pathway databases. We illustrate with examples how this can aid in identifying important processes from large complex lists.
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4.
Meta-analysis added power to identify variants in FTO associated with type 2 diabetes and obesity in the Asian population.
Liu, Y, Liu, Z, Song, Y, Zhou, D, Zhang, D, Zhao, T, Chen, Z, Yu, L, Yang, Y, Feng, G, et al
Obesity (Silver Spring, Md.). 2010;(8):1619-24
Abstract
Several common variants in the intron 1 of FTO (fat mass and associated obesity) gene have been reliably associated with BMI and obesity in European populations. We analyzed two variants (rs9939609 and rs8050136) in 4,189 Chinese Han individuals and conducted a meta-analysis of published studies in Asian population to investigate whether these variants are associated with type 2 diabetes (T2D) and obesity in Asian population. In this study, both the minor allele A of rs9939609 and the minor allele A of rs805136 were associated with increased risk of T2D, independent of measures of BMI; the odds ratios (ORs) per copy of the risk allele were 1.19 for rs9939609 (95% confidence interval (CI), 1.04-1.37; P = 0.01) and 1.22 for rs8050136 (95% CI, 1.07-1.40; P = 0.004) after adjusting for age, sex, and BMI. Our results also showed association with risk of obesity (rs9939609: OR = 1.39 (95% CI 1.04-1.85), P = 0.02; rs8050136: OR = 1.45 (95% CI 1.09-1.93), P = 0.01) but no association with overweight. These results were consistent with the pooled results from our meta-analysis study (for diabetes, rs8050136, P = 1.3 x 10(-3); rs9939609, P = 9.8 x 10(-4); for obesity, rs8050136, P = 2.2 x 10(-7); rs9939609, P = 9.0 x 10(-9)). Our findings indicate that the two variants (rs9939609 and rs8050136) in the FTO gene contribute to obesity and T2D in the Asian populations.
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5.
[Separation of proteins on microchip electrophoresis and its comparison with DNA migration].
Liu, C, Xu, X, Zhang, J, Chen, J
Se pu = Chinese journal of chromatography. 2010;(3):296-300
Abstract
The efficient separation of six standard proteins on a home-made poly (dimethylsiloxane) microchip with an auto-deducting background diode laser induced fluorescence detector was accomplished within 6.4 min under the sieving matrix of 10 g/L hydroxyethyl cellulose (HEC), 1 g/L sodium dodecyl sulphonate (SDS), 40 mmol/L phosphate buffer at pH 7.0. The experimental results showed that the reproducibility of protein separation was satisfactory and the relative standard deviations (RSDs) of protein migration time were less than 10%. The migration times of the proteins are analyzed by a quantitative mathematical model of deoxyribonucleic acid (DNA) proposed by ourselves previously. The results showed that the migration character of SDS-protein complexes was similar with DNA. However, the linear relationships between the mobilities of SDS-protein complexes and their relative molecular mass as well as electric field strength became worse, which indicated the mathematical model for DNA separation should be revised before it is used for protein separation.