An integrated approach for the analysis of biological pathways using mixed models

Gene class, ontology, or pathway testing analysis has become increasingly popular in microarray data analysis. Such approaches allow the integration of gene annotation databases, such as Gene Ontology and KEGG Pathway, to formally test for subtle but coordinated changes at a system level. Higher power in gene class testing is gained by combining weak signals from a number of individual genes in each pathway. We propose an alternative approach for gene-class testing based on mixed models, a class of statistical models that: a) provides the ability to model and borrow strength across genes that are both up and down in a pathway, b) operates within a well-established statistical framework amenable to direct control of false positive or false discovery rates, c) exhibits improved power over widely used methods under normal location-based alternative hypotheses, and d) handles complex experimental designs for which permutation resampling is difficult. We compare the properties of this mixed models approach with nonparametric method GSEA and parametric method PAGE using a simulation study, and illustrate its application with a diabetes data set and a dose-response data set.     

Autophagy protects LNCaP cells under androgen deprivation conditions

Androgen plays a critical role in the development and progression of prostate cancer. However, the regulatory role of androgen in the autophagic process and the function of the increased autophagosomes following androgen deprivation remain poorly understood. We found that autophagosomes, which were induced upon serum deprivation in LNCaP cells, can be significantly suppressed by dihydrotestosterone (DHT). Pharmacological inhibition of autophagy by 3-methyladenine led to increased apoptosis of LNCaP cells in serum-free medium compared to the medium with DHT or serum. Additionally, depletion of Beclin 1 to inhibit autophagy by small interfering RNA resulted in a slower proliferation of LNCaP cells in the medium depleted of serum than in the medium with DHT. Altogether, these findings suggested that LNCaP cells can resort to the autophagic pathway to survive under androgen deprivation conditions, which can be a novel mechanism involved in the transition of prostate cancer cells from an androgen-dependent to an androgen-independent cell type.     

检测心肌细胞钾离子通道蛋白活化水平方法的优化

介绍了一种如何合理的利用蛋白质免疫沉淀和蛋白质免疫印迹相结合的方法检测大鼠心肌细胞钾离子通道蛋白Kv1.2和Kv1.5的表达与活化水平.实验结果表明,与单独利用免疫印迹的方法相比较,本实验是对钾离子通道蛋白及其它亚家族的钾通道蛋白磷酸化表达水平检测方法的一种优化,从而获得一套可行、简单、合理的实验方案,同时也提高了检测的准确性,敏感性及特异性.     

Enhancement of RNAi by a small molecule antibiotic enoxacin

Dear Editor,
RNAi has become a mainstream molecular tool for assessing the functions of genes in mammalian cells . Large-scale RNA interference-based analyses are often complicated by false positive and negative hits due to off-target effects and interferon response , which can be attributed at least in part to the use of high concentrations of siRNA. Lowering the amounts of siRNAs and shRNAs can effectively and expediently mitigate the off-target effect and interferon response .     

假马齿苋的组织培养

1植物名称假马齿苋[Bacoba monnieri（L．）Wettst．],又名白花猪母菜、白线草、蛇鳞菜。 2材料类别茎尖。     

Lovastatin protects mesenchymal stem cells against hypoxia- and serum deprivation-induced apoptosis by activation of PI3K/Akt and ERK1/2

Cell therapy with bone marrow-derived mesenchymal stem cells (MSCs) has been shown to have great promises in cardiac repair after myocardial infarction. However, poor viability of transplanted MSCs in the infracted heart has limited the therapeutic efficacy. Our previous studies have shown in vitro that rat MSCs undergo caspase-dependent apoptosis in response to hypoxia and serum deprivation (Hypoxia/SD). Recent findings have implicated statins, an established class of cholesterol-lowering drugs, enhance the survival of cells under various conditions. In this study, we investigated the effect of lovastatin on rat MSCs apoptosis induced by Hypoxia/SD, focusing in particular on regulation of mitochondrial apoptotic pathway and the survival signaling pathways. We demonstrated that lovastatin (0.01-1 microM) remarkably prevented MSCs from Hypoxia/SD-induced apoptosis through inhibition of the mitochondrial apoptotic pathway, leading to attenuation of caspase-3 activation. The loss of mitochondrial membrane potential and cytochrome-c release from mitochondria to cytosol were significantly inhibited by lovastatin. Furthermore, the antiapoptotic effect of lovastatin on mitochondrial apoptotic pathway was effectively abrogated by both PI3K inhibitor, LY294002 and ERK1/2 inhibitor, U0126. The phosphorylations of Akt/GSK3 beta and ERK1/2 stimulated by lovastatin were detected. The activation of ERK1/2 was inhibited by a PI3K inhibitor, LY294002, but U0126, a ERK1/2 inhibitor did not inhibit phosphorylation of Akt and GSK3 beta. These data demonstrate that lovastatin protects MSCs from Hypoxia/SD-induced apoptosis via PI3K/Akt and MEK/ERK1/2 pathways, suggesting that it may prove a useful therapeutic adjunct for transplanting MSCs into damaged heart after myocardial infarction.     

Specific LPA receptor subtype mediation of LPA-induced hypertrophy of cardiac myocytes and involvement of Akt and NFkappaB signal pathways

Lysophosphatidic acid (LPA) is a bioactive phospholipid with diverse functions mediated via G-protein-coupled receptors (GPCRs). In view of the elevated levels of LPA in acute myocardial infarction (MI) patients we have conducted studies aimed at identifying specific LPA receptor subtypes and signaling events that may mediate its actions in hypertrophic remodeling. Experiments were carried out in cultured neonatal rat cardiomyocytes (NRCMs) exposed to LPA and in a rat MI model. In NRCMs, LPA-induced hypertrophic growth was completely abrogated by DGPP, an LPA1/LPA3 antagonist. The LPA3 agonist OMPT, but not the LPA2 agonist dodecylphosphate, promoted hypertrophy as examined by 3[H]-Leucine incorporation, ANF-luciferase expression and cell area. In in vivo experiments, LPA1, LPA2 and LPA3 mRNA levels as well as LPA1 and LPA3 protein levels increased together with left ventricular remodeling (LVRM) after MI. In addition, LPA stimulated the phosphorylation of Akt and p65 protein and activated NF-kappaB-luciferase expression. Inhibitors of PI3K (wortmannin), mTOR (rapamycin), and NF-kappaB (PDTC or SN50) effectively prevented LPA-induced 3[H]-Leucine incorporation and ANF-luciferase expression. Furthermore, ERK inhibitors (U0126 and PD98059) suppressed LPA-stimulated activation of NF-kappaB and p65 phosphorylation whereas wortmannin showed no effect on NF-kappaB activation. Our findings indicate that LPA3 and/or LPA1 mediate LPA-induced hypertrophy of NRCMs and that LPA1 and LPA3 may be involved in LVRM of MI rats. Moreover, Akt and NF-kappaB signaling pathways independently implicate in LPA-stimulated myocardial hypertrophic growth.     

Stem cells in development of therapeutics for Parkinson's disease: a perspective

Using Parkinson's disease as a prototype of neurodegenerative diseases, we propose applications of human stem cells in the development of therapeutics for neurodegenerative diseases. First, in vitro differentiation of human stem cells offers a versatile model for dissecting molecular interactions underlying human dopamine (DA) neuron specification, which may form a foundation for instigating regeneration of DA neurons from progenitors that reside in the brain. Second, stem cells derived from diseased cells or through genetic modification can serve as a platform for unraveling biochemical processes that lead to the cellular pathogenesis of degeneration. This may in turn serve as a template for identifying or developing therapeutics for slowing, stopping, or reversing the disease process. And finally, stem cells, particularly those induced from patients' own cells, provide a reliable source of DA neurons for cell-based therapy.