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Biomarker Analysis (biomarker + analysis)
Selected AbstractsMicrobial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateauENVIRONMENTAL MICROBIOLOGY, Issue 10 2007Hongchen Jiang Summary Previous investigations of the salinity effects on the microbial community composition have largely been limited to dynamic estuaries and coastal solar salterns. In this study, the effects of salinity and mineralogy on microbial community composition was studied by using a 900-cm sediment core collected from a stable, inland hypersaline lake, Lake Chaka, on the Tibetan Plateau, north-western China. This core, spanning a time of 17 000 years, was unique in that it possessed an entire range of salinity from freshwater clays and silty sands at the bottom to gypsum and glauberite in the middle, to halite at the top. Bacterial and archaeal communities were studied along the length of this core using an integrated approach combining mineralogy and geochemistry, molecular microbiology (16S rRNA gene analysis and quantitative polymerase chain reaction), cultivation and lipid biomarker analyses. Systematic changes in microbial community composition were correlated with the salinity gradient, but not with mineralogy. Bacterial community was dominated by the Firmicutes -related environmental sequences and known species (including sulfate-reducing bacteria) in the freshwater sediments at the bottom, but by halophilic and halotolerant Betaproteobacteria and Bacteroidetes in the hypersaline sediments at the top. Succession of proteobacterial groups along the salinity gradient, typically observed in free-living bacterial communities, was not observed in the sediment-associated community. Among Archaea, the Crenarchaeota were predominant in the bottom freshwater sediments, but the halophilic Halobacteriales of the Euryarchaeota was the most important group in the hypersaline sediments. Multiple isolates were obtained along the whole length of the core, and their salinity tolerance was consistent with the geochemical conditions. Iron-reducing bacteria were isolated in the freshwater sediments, which were capable of reducing structural Fe(III) in the Fe(III)-rich clay minerals predominant in the source sediment. These data have important implications for understanding how microorganisms respond to increased salinity in stable, inland water bodies. [source] Potential biomarkers involving IKK/RelA signal in early stage non-small cell lung cancerCANCER SCIENCE, Issue 3 2008Xianqing Jin The clinical relevance of nuclear factor ,B (NF-,B) and its regulatory molecules on prognosis of patient with early stages of non-small cell lung cancer (NSCLC), remains unclear. Therefore, we conducted biomarker analyses with survival in patients with stages I and II NSCLC. Tumor samples were collected from 88 patients with early-stage NSCLC (stages I, II). A minimum follow-up period of 5 years was required. RelA, phosphorylated I,B (pI,B,), pIKK,/, were detected by immunostaining. NF-,B DNA binding activity was assessed by electrophoretic mobility shift assay. Association of clinical and pathologic variables (e.g. sex, age, pathologic stage) with relevant molecules was determined by Pearson's ,2 test or Fisher's exact test. Survival analysis based on single expression of RelA, pI,B,, pIKK,/, as well as composite expressions were evaluated using Cox proportional hazards regression models, and log rank test followed Kaplan-Meier estimates. RelA, pI,B,, pIKK,/, were observed as increased expression in NSCLC tissues compared with adjacent normal tissues and normal lung tissues. These molecules were associated with tumor-node-metastasis stages, T stages and histological status, respectively. Among the molecules analyzed, RelA and pI,B,-positive were statistically significant predictors of patient death in the entire patient population adjusted by age, gender and smoking status; furthermore both RelA and pI,B,-positive was the strongest prognostic indicators of poor prognosis by univariate and multivariate analyses. Borderline positive correlations were observed between RelA and pI,B, or pIKK,/, expression. In this cohort of early-stage NSCLC patients, molecular markers, especially composite application of multiple biomarkers (both nuclear RelA and cytoplasmic pI,B-, expression) that independently predict overall survival have been identified. (Cancer Sci 2008; 99: 582,589) [source] Assessing the toxicity of TBBPA and HBCD by zebrafish embryo toxicity assay and biomarker analysisENVIRONMENTAL TOXICOLOGY, Issue 4 2009Jun Hu Abstract Tetrabromobisphenol A (TBBPA) and hexabromocyclododecane (HBCD) are two of the most widely used brominated flame retardants (BFRs). The biological toxicity effect of TBBPA and HBCD was studied by means of zebrafish embryo toxicity assays in combination with three biomarkers, including superoxide dismutase (SOD), lipid peroxidation, (LPO), and heat shock protein (Hsp70). The standard zebrafish embryo assay showed that high concentrations of TBBPA (,0.75 mg/L) can cause lethality or malformation. For HBCD within the concentration range (0.002,10 mg/L), no endpoint was observed. Furthermore, SOD activities of zebrafish embryos exposed to TBBPA were increased with the increasing concentrations. SOD activities in the group treated by HBCD showed an increase followed by a decline. Regardless of TBBPA or HBCD, LPO were increased along with the increase of the concentration. The change pattern of Hsp70 levels was the same with LPO. All these results showed that TBBPA and HBCD could cause oxidative stress and Hsp70 overexpression, inducing acute toxicity to zebrafish embryo in a short-term exposure. The study also indicates that the zebrafish embryo assay in combination with the biomarkers is effective in aquatic environmental toxicology and risk assessment. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009. [source] Analysis of endogenous glutathione-adducts and their metabolitesBIOMEDICAL CHROMATOGRAPHY, Issue 1 2010Ian A. Blair Abstract The ability to conduct validated analyses of glutathione (GSH)-adducts and their metabolites is critically important in order to establish whether they play a role in cellular biochemical or pathophysiological processes. The use of stable isotope dilution (SID) methodology in combination with liquid chromatography,tandem mass spectrometry (LC-MS/MS) provides the highest bioanalytical specificity possible for such analyses. Quantitative studies normally require the high sensitivity that can be obtained by the use of multiple reaction monitoring (MRM)/MS rather than the much less sensitive but more specific full scanning methodology. The method employs a parent ion corresponding to the intact molecule together with a prominent product ion that obtained by collision induced dissociation. Using SID LC-MRM/MS, analytes must have the same relative LC retention time to the heavy isotope internal standard established during the validation procedure, the correct parent ion and the correct product ion. This level of specificity cannot be attained with any other bioanalytical technique employed for biomarker analysis. This review will describe the application of SID LC-MR/MS methodology for the analysis of GSH-adducts and their metabolites. It will also discuss potential future directions for the use of this methodology for rigorous determination of their utility as disease and exposure biomarkers. Copyright © 2010 John Wiley & Sons, Ltd. [source] Laser-capture microdissection in prostate cancer research: establishment and validation of a powerful tool for the assessment of tumour,stroma interactionsBJU INTERNATIONAL, Issue 6 2008Chitranjan J. Shukla OBJECTIVES To describe our experience with the optimization and validation of laser-capture microdissection (LCM) for biomarker analysis in prostate tissues. As LCM allows the separation of benign and malignant epithelial structures and stromal elements, it not only allows identification of the source of the biomarker, but might also accentuate gene or protein expression changes by reducing contamination by other cellular elements. MATERIALS AND METHODS In all, 19 fresh-frozen prostate tissue samples were subjected to LCM, with the cDNA being analysed using quantitative polymerase chain reaction for several genes, to identify the optimum number of cells for capture, as well as gene markers assessing for the purity of the captured cells. The localization was further confirmed by in situ hybridization. RESULTS Prostate-specific antigen (PSA) and cytokeratin 8, were expressed solely by epithelial cells, whereas hepatocyte growth factor (HGF) and tissue inhibitor of metalloproteinases-3 (TIMP3) were expressed only by stromal cells, and the levels of transcripts of these genes were unaltered between benign and malignant tissues. CONCLUSIONS These data suggest that PSA, cytokeratin 8, HGF and TIMP3 are reliable gene markers of purity of epithelial and stromal compartments for LCM of prostate tumours. Although this technique is not new and is increasingly used in laboratories, it needs optimization and stringent validation criteria before data analysis. This applies to all tissue types subjected to LCM. [source] | ||||||||||