Trypsin digest coupled with two-dimensional shotgun proteomics reveals the involvement of multiple signaling pathways in functional remodeling of late-gestation uteri in rats

Pregnant uteri become quiescent after functional remodeling but details are not fully known. Here we revealed uterine proteins of late-gestation rats by 2-D shotgun proteomic analysis and correlated protein expression with uterine functions. After duplication, 239 proteins were identified. About 190 proteins commonly found in duplicate analyses were subjected to functional annotation. The proteins associated with signal transduction fell into three known pathways. Western blotting and functional data indicated that: (i) a reduction of Na(+)/K(+)-ATPase-related proteins was associated with the decrease of contraction rate, (ii) a reduction of tyrosine hydroxylase and cyclic AMP-dependent protein kinase type II-alpha regulatory chain (PKARII alpha) was associated with an increase in the relaxation response to 8-bromo-cAMP, and (iii) in the presence of Ras, an increased expression of nucleolin was associated with the elevation of Bcl-xL, an antiapoptotic protein. In conclusion, 2-D shotgun proteomic analysis provides a global database of uterine proteins for hypothesis-driven studies. Our data suggest that in late-gestation uteri down-regulation of PKARII alpha and Na(+)/K(+)-ATPase may cause functional remodeling and lead to uterine quiescent. Up-regulation of antiapoptotic proteins (nucleolin and Bcl-xL) in the Ras-mediated pathway may maintain cell survival and counteract cell loss during remodeling.     

Drp1的调控对PINK1突变转基因果蝇的保护作用

帕金森病（PD）是以黑质致密部多巴胺神经元选择性减少和胞浆内路易小体的形成为特征的神经退行性疾病。研究发现,PTEN诱导激酶1(PINK1)基因突变导致家族性早发型帕金森病的发生。在转基因果蝇中,PINK1功能丢失导致间接飞行肌缺陷,线粒体结构、功能障碍,多巴胺神经元丢失。本研究在PINK1突变PD转基因果蝇中,进行发动蛋白相关蛋白1（Drp1）过表达和敲低,探索Drp1对PD转基因果蝇的保护作用及其可能机制。本研究选用MHC-Gal4/UAS系统的PD转基因果蝇模型,特异性启动PINK1B9基因于果蝇肌肉组织中表达;运用Drp1基因过表达和RNA干扰干预PINK1B9转基因果蝇,研究其对PD转基因果蝇的作用。结果显示,不论过表达Drp1还是Drp1敲低均可挽救PINK1突变转基因果蝇,降低翅膀异常率,改善飞行能力,恢复间接飞行肌排列,调节线粒体形态,提高ATP生成量,上调NDUFS3蛋白表达水平。本文结果提示,Drp1的调控挽救PINK1突变转基因果蝇与线粒体呼吸链有关。     

The various effects of fractionated oxidized low density lipoproteins on the growth of smooth muscle cells in culture

The effects of fractionated oxidized low density lipoproteins (oxidized LDL) on the growth of vascular smooth muscle cells (VSMC) and their relationship to the formation of lysophosphatidylcholine (lyso-PC) as well as the activation of protein kinase C (PKC) were studied. VSMC were isolated from porcine aorta by explant culture. LDL was isolated from porcine blood by sequential ultracentrifugation and oxidized LDL was obtained by incubating LDL with 5 µM CuSO₄ at 37° C for various lengths of time. Our results showed that LDL oxidized for 12 h and eluted from fast protein liquid chromatography at 43 min inhibited the growth of VSMC, and that LDL oxidized for longer than 48 h and eluted at 48 min stimulated the growth of VSMC. The formation of lyso-PC in the oxidized LDL correlated well with its stimulatory effect, suggesting that lyso-PC is responsible for the mitogenic effect of oxidized LDL. This stimulatory effect of oxidized LDL was inhibited by staurosporine, a PKC inhibitor. Treatment with oxidized LDL increased the activity of membrane PKC, but it decreased that of cytosolic PKC, suggesting the translocation of PKC from cytosol to the membrane in the presence of oxidized LDL. These results suggested that the oxidized LDL-stimulated VSMC growth was mediated by the formation of lyso-PC and the activation of PKC.     

Split-Plot Microarray Experiments

This article focuses on microarray experiments with two or more factors in which treatment combinations of the factors corresponding to the samples paired together onto arrays are not completely random. A main effect of one (or more) factor(s) is confounded with arrays (the experimental blocks). This is called a split-plot microarray experiment. We utilise an analysis of variance (ANOVA) model to assess differentially expressed genes for between-array and within-array comparisons that are generic under a split-plot microarray experiment. Instead of standard t- or F-test statistics that rely on mean square errors of the ANOVA model, we use a robust method, referred to as 'a pooled percentile estimator', to identify genes that are differentially expressed across different treatment conditions. We illustrate the design and analysis of split-plot microarray experiments based on a case application described by Jin et al. A brief discussion of power and sample size for split-plot microarray experiments is also presented.     

Effects of different intensities of extremely low frequency pulsed electromagnetic fields on formation of osteoclast-like cells

Over the past 30 years, the beneficial therapeutic effects of selected low energy, time varying electromagnetic fields (EMF) have been documented with increasing frequency to treat therapeutically resistant problems of the musculoskeletal system. However, the underlying mechanisms at a cellular level are still not completely understood. In this study, the effects of extremely low frequency pulsed electromagnetic fields (ELF-PEMF) on osteoclastogenesis, cultured from murine bone marrow cells and stimulated by 1,25(OH)(2)D(3), were examined. Primary bone marrow cells were cultured from mature Wistar rats and exposed to ELF-PEMF stimulation daily for 7 days with different intensities of induced electric field (4.8, 8.7, and 12.2 micro V/cm rms) and stimulation times (0.5, 2, and 8 h/day). Recruitment and authentication of osteoclast-like cells were evaluated, respectively, by determining multinuclear, tartrate resistant acid phosphatase (TRAP) positive cells on day 8 of culture and by the pit formation assay. During the experiments, cytokines such as tumor necrosis factor-alpha (TNF-alpha), interleukin 1-beta (IL-1beta), and prostaglandin-E(2) (PGE(2)) were assayed using the enzyme linked immunosorbent assay (ELISA). These findings suggest that ELF-PEMF can both enhance (approximately 50%) and suppress (approximately 27%) the formation of osteoclast-like cells in bone marrow culture, depending on the induced electric field intensity. In addition, consistent correlations were observed between TNF-alpha, IL-1beta, and osteoclast-like cell number after exposure to different induced electric field intensities of ELF-PEMF. This in vitro study could be considered as groundwork for in vivo ELF-PEMF clinical applications on some osteoclast-associated bone diseases.     

Incorporation of clustering effects for the Wilcoxon rank sum test: a large-sample approach

The Wilcoxon rank sum test is frequently used in statistical practice for the comparison of measures of location when the underlying distributions are far from normal or not known in advance. An assumption of the ordinary rank sum test is that individual sampling units are independent. In many ophthalmologic clinical trials, the Early Treatment for Diabetic Retinopathy Scale (ETDRS) is a principal endpoint used for measuring the level of diabetic retinopathy. This is an ordinal scale, and it is natural to consider the Wilcoxon rank sum test for the comparison of the level of diabetic retinopathy between treatment groups. However, under this design, unlike the usual Wilcoxon rank sum test, the subject is the unit of randomization, but the eye is the unit of analysis. Furthermore, a person will tend to have different, but correlated, ETDRS scores for fellow eyes. Thus, we propose a correction to the variance of the Wilcoxon rank sum statistic that accounts for clustering effects and that can be used for both balanced (same number of subunits per cluster) or unbalanced (different number of subunits per cluster) data, both in the presence or absence of ties, with p-value adjusted accordingly. In this article, we present large-sample theory and simulation results for this test procedure and apply it to diabetic retinopathy data from type I diabetics in the Sorbinil Retinopathy Trial.     

Alternations of Metabolic Profile and Kynurenine Metabolism in the Plasma of Parkinson’s Disease

The pathogenesis of Parkinson’s disease (PD) remains to be elucidated. Metabolomic analysis has the potential to identify biochemical pathways and metabolic profiles that are involved in PD pathogenesis. Here, we performed a targeted metabolomics to quantify the plasma levels of 184 metabolites in a discovery cohort including 82 PD patients and 82 normal controls (NCs) and found two up-regulated (dopamine, putrescine/ornithine ratio) and four down-regulated (octadecadienylcarnitine C18:2, asymmetric dimethylarginine, tryptophan, and kynurenine (KYN)) metabolites in the plasma of PD patients. We then measured the plasma levels of a panel of metabolic products of KYN pathway in an independent validation cohort including 118 PD patients, 22 Huntington’s disease (HD) patients, and 37 NCs. Lower kynurenic acid (KA)/KYN ratio, higher quinolinic acid (QA) level, and QA/KA ratio were observed in PD patients compared to HD patients and NCs. PD patients at advanced stage (Hoehn-Yahr stage >?2) showed lower KA and KA/KYN ratio, as well as higher QA and QA/KA ratio compared to PD patients at early stage (Hoehn-Yahr stage ≤?2) and NCs. Levels of KA and QA, as well as the ratios of KA/KYN and QA/KA between PD patients with and without psychiatric symptoms, dementia, or levodopa-induced dyskinesia in the advanced PD were similar. This metabolomic analyses demonstrate a number of plasma biomarker candidates for PD, suggesting a shift toward neurotoxic QA synthesis and away from neuroprotective KA production in KYN pathway.