Metabolites offer an important unexplored complement to understanding the pluripotency of stem cells. Using mass spectrometry-based metabolomics, we show that embryonic stem cells are characterized by abundant metabolites with highly unsaturated structures whose levels decrease upon differentiation. By monitoring the reduced and oxidized glutathione ratio as well as ascorbic acid levels, we demonstrate that the stem cell redox status is regulated during differentiation. Based on the oxidative biochemistry of the unsaturated metabolites, we experimentally manipulated specific pathways in embryonic stem cells while monitoring the effects on differentiation. Inhibition of the eicosanoid signaling pathway promoted pluripotency and maintained levels of unsaturated fatty acids. In contrast, downstream oxidized metabolites (e.g., neuroprotectin D1) and substrates of pro-oxidative reactions (e.g., acyl-carnitines), promoted neuronal and cardiac differentiation. We postulate that the highly unsaturated metabolome sustained by stem cells makes them particularly attuned to differentiate in response to in vivo oxidative processes such as inflammation.

Mass spectrometry based metabolomics represents a new area for bioinformatics technology development. While the computational tools currently available such as XCMS statistically assess and rank LC-MS features, they do not provide information about their structural identity. XCMS 2 is an open source software package which has been developed to automatically search tandem mass spectrometry (MS/MS) data against high quality experimental MS/MS data from known metabolites contained in a reference library (METLIN). Scoring of hits is based on a "shared peak count" method that identifies masses of fragment ions shared between the analytical and reference MS/MS spectra. Another functional component of XCMS 2 is the capability of providing structural information for unknown metabolites, which are not in the METLIN database. This "similarity search" algorithm has been developed to detect possible structural motifs in the unknown metabolite which may produce characteristic fragment ions and neutral losses to related reference compounds contained in METLIN, even if the precursor masses are not the same.Liquid chromatography mass spectrometry (LC-MS) combined with comprehensive quantitative data analysis has allowed LC-MS to become the primary platform for metabolic profiling experiments. 1,2 However, even as "shotgun" proteomic data analysis has evolved over the past decade, 3 metabolomics is still in the beginning stages of its' informatic development. Metabolomics experiments are traditionally targeted, where specific metabolites are quantified, and untargeted metabolomics experiments include relative quantification of all observed metabolites. We have termed the combination of these strategies "sniper" metabolomics, where initial LC-MS metabolite profiles are followed by LC-MS/MS experiments on selected, highly differentiated targets. The resulting output from a typical "sniper" metabolomics experiment is the statistical evaluation of the most significantly changing metabolites followed by their structural identification.A common goal of most bioinformatic platforms in metabolomics is to allow users to find and statistically assess features that show significant change between sample groups. The most significant features are then selected for targeted tandem MS (MS/MS) analysis, thereby guaranteeing high quality MS/MS data which provides high confidence to data interpretation. Recently, three different open source MS based metabolite profiling software packages were released including XCMS, 1 MathDAMP, 4 and Met-IDEA. 5 Met-IDEA and MathDAMP both have differential analysis capabilities and present useful platforms for GC and LC-MS analysis. MathDAMP takes advantage of the language Mathematica to present data in a variety of graphical representations. Met-IDEA is written in Microsoft's ".NET" language and features a simple, user-friendly interface that accepts capillary electrophoresis mass spectrometry data. Instrument manufacturers have also produced software packages for metabolomics including * To whom corres...

73% of patients with apparently unidentifiable causes for HCC were HBV-related. The detection rate was higher in nontumorous tissues than tumorous tissues. The low intrahepatic HBV DNA and pgRNA levels indicated that persistent viral replication and possibly HBV integration are the likely causes of HCC in OBI patients.

A rapid and inexpensive method for estimating lipid content of yeasts is needed for screening large numbers of yeasts samples. Nile red is a fluorescent lipophilic dye used for detection and quantification of intracellular lipid droplets in various biological system including algae, yeasts and filamentous fungi. However, a published assay for yeast is affected by variable diffusion across the cell membrane, and variation in the time required to reach maximal fluorescence emission. In this study, parameters that may influence the emission were varied to determine optimal assay conditions. An improved assay with a high-throughput capability was developed that includes the addition of dimethyl sulfoxide (DMSO) solvent to improve cell permeability, elimination of the washing step, the reduction of Nile red concentration, kinetic readings rather than single time-point reading, and utilization of a black 96-well microplate. The improved method was validated by comparison to gravimetric determination of lipid content of a broad variety of ascomycete and basidiomycete yeast species.

Abstract-Ecotoxicological assessments of contaminated soil aim to understand the effect of introduced chemicals on the soil flora and fauna. Ecotoxicity test methods were developed and conducted on hydrocarbon-contaminated soils (Ͻ5,000-30,000 mg/kg total petroleum hydrocarbon) and on adjacent uncontaminated control soils from eight field locations. Tests included 7-d, 14-d, and chronic survival tests and reproduction assays for the earthworm (Eisenia fetida) and seed germination, root length, and plant growth assays for corn, lettuce, mustard, and wheat. Species-specific responses were observed with no-observed effect concentrations (NOECs) ranging from Ͻ1 to 100% contaminated soil. The 14-d earthworm survival NOEC was equal to or greater than the reproduction NOEC values for numbers of cocoons and juveniles, which were similar to one another. Cocoon and juvenile production varied among the control soils. Germination and root length NOECs for mustard and lettuce were less than NOECs for corn and wheat. Root length NOECs were similar to or less than seed germination NOECs. Statistically significant correlations (p Ͻ 0.05) for earthworm survival and seed germination as a function of hydrocarbon measurements were found. The 14-d earthworm survival and the seed germination tests are recommended for use in the context of a risk-based framework for the ecological assessment of contaminated sites.

BACKGROUND:Helicobacter pylori infection causes gastric mucosal inflammatory responses, resulting in up-regulation of interleukin1b (IL-1b) and overproduction of mutagenic nitric oxide (NO). The authors previously demonstrated that IL-1b plays an important role in H. pylori-induced E-cadherin (E-cad) methylation. Here, they extend the study to investigate the downstream effect of IL-1b on H. pylori-induced gastric inflammation and aberrant DNA methylation. METHODS: Human gastric cancer cell lines (MKN7, MKN74, and TMK-1) with and without pretreatment of IL-1 receptor antagonist (IL-1ra) were treated with IL-1b or infected with H. pylori. Promoter methylation status of E-cad was examined by methylation-specific polymerase chain reaction (PCR). Expression of E-cad, inducible nitric oxide synthase (iNOS), and nuclear factor jB (NFjB) was assessed by quantitative reverse transcriptase PCR, Western blotting, or immunofluorescence. NO production and total DNA methyltransferase (DNMT) activity were assayed fluorometrically. RESULTS: Both IL-1b treatment and H. pylori infection-induced E-cad methylation led to a decrease in E-cad expression at both mRNA and protein levels. Total DNMT enzymatic activity was significantly elevated in treated cells, accounting for the observed E-cad methylation induction. Increased expression of NFjB was accompanied by up-regulation of iNOS and production of NO in treated cells. Reversal of all these phenomena in cells pretreated with IL-1ra suggested H. pylori-induced E-cad methylation via IL-1b stimulation of the NFjB transcriptional system, leading to activation of DNMT activity by NO production. CONCLUSIONS: These findings reveal a previously unknown effect of IL-1b and NO on H. pylori-induced aberrant DNA methylation. This possible pathway indicates the role of NO in epigenetic modification that links inflammation to carcinogenesis. Cancer 2012;118:4969-80.

Here we describe the first phenotypic screening with microalgae to study lipid metabolism and to discover organic small molecules as chemical triggers that increase growth and lipid production. A microplate assay has been developed for analysis of intracellular lipids using Nile Red fluorescence in order to screen a collection of diverse bioactive organic molecules (e.g., kinase inhibitors) with four strains of oleaginous microalgae (Nannochloropsis salina, Nannochloropsis oculata, Nannochloris sp., and Phaeodactylum tricornutum). Several small molecules identified in microplate screening increased lipid productivity >200% without decreasing growth and biomass production. Selected compounds were further investigated in the context of larger batch culture experiments (e.g., 500 mL) and demonstrated to increase lipid levels (up to 84%) while maintaining or increasing the specific growth rate. Bioactive molecules such as forskolin and quinacrine were identified as promising probes of microalgae lipid pathways. We have also determined that common antioxidants such as epigallocatechin gallate and butylated hydroxyanisole (BHA) increase lipid productivity and may represent new probes of oxidative signaling pathways for photooxidative protection.

Objectives:We aimed to determine the levels of alanine aminotransferase (ALT), hepatitis B virus DNA (HBV DNA), HBsAg, and a novel viral marker (hepatitis B core-related antigen (HBcrAg)); hepatitis B e antigen (HBeAg) seroconversion and drug resistance rates after 7 years of entecavir treatment in chronic hepatitis B (CHB) patients.Methods:Two hundred and twenty-two Chinese CHB patients on continuous entecavir treatment were recruited. Serologic, virologic, biochemical outcomes, and the occurrence of entecavir signature mutations were determined.Results:The rates of ALT normalization, HBeAg seroconversion, and undetectable HBV DNA were 98.3%, 82.1%, and 98.7%, respectively, after 7 years of entecavir treatment. The genotypic resistance rate was 1.2%. Decline of HBsAg level was modest with a median decline rate of 0.107 log IU/ml/year. Among patients with baseline HBsAg <1,000 IU/ml and annual HBsAg decline rate of ≥0.166 log IU/ml, all have HBsAg of <200 IU/ml (a level highly predictive for HBsAg seroclearance) at year 7. In contrast, in patients with baseline HBsAg ≥1,000 IU/ml and annual HBsAg decline rate of <0.166 log IU/ml, 95.5% had HBsAg of ≥200 IU/ml at year 7. Decline of HBcrAg levels was moderate with a median decline rate of 0.244 log kU/ml/year. Forty-seven patients (32.0%) had undetectable HBcrAg level at year 7.Conclusions:Long-term entecavir therapy continued to have good responses with low drug resistance rate. However, the decline of HBsAg with treatment was suboptimal. HBcrAg level declined at a relatively better rate. Baseline HBsAg level of <1,000 IU/ml and annual decline of 0.166 log IU/ml could be used to predict HBsAg response.