Oxidative defense metabolites induced by salinity stress in roots of Salicornia herbacea.

High salinity is a major abiotic stress that affects the growth and development of plants. This type of stress can influence flowering, the production of crops, defense mechanisms and other physiological processes. Previous studies have attempted to elucidate salt-tolerance mechanisms to improve plant growth and productivity in the presence of sodium chloride. One such plant that has been studied in detail is Salicornia, a well-known halophyte, which has adapted to grow in the presence of high salt. To further the understanding of how Salicornia grows and develops under high saline conditions, Salicornia herbacea (S. herbacea) was grown under varying saline concentrations (0, 50, 100, 200, 300, and 400mM), and the resulting phenotype, ion levels, and metabolites were investigated. The optimal condition for the growth of S. herbacea was determined to be 100mM NaCl, and increased salt concentrations directly decreased the internal concentrations of other inorganic ions including Ca2+, K+, and Mg2+. Metabolomics were performed on the roots of the plant as a systematic metabolomics study has not yet been reported for Salicornia roots. Using ethylacetate and methanol extraction followed by high resolution ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS), 1793 metabolites were identified at different NaCl levels. Structural and functional analyses demonstrated that the concentration of 53 metabolites increased as the concentration of NaCl increased. These metabolites have been linked to stress responses, primarily oxidative stress responses, which increase under saline stress. Most metabolites can be classified as polyols, alkaloids, and steroids. Functional studies of these metabolites show that shikimic acid, vitamin K1, and indole-3-carboxylic acid are generated as a result of defense mechanisms, including the shikimate pathway, to protect against reactive oxygen species (ROS) generated by salt stress. This metabolite profiling provides valuable information on the salt-tolerance mechanisms of S. herbacea and may be applied to bioengineer plants with improved salt tolerance.

A Dual Readout Assay Based on Fluorescence Polarization and Time-Resolved Fluorescence Resonance Energy Transfer to Screen for RSK1 Inhibitors.

A dual readout assay based on fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET) exhibits many advantages over single assay technology in terms of screening quality and efficiency. In this study, we developed a dual readout assay combining FP and TR-FRET to identify ribosomal S6 kinase 1 (RSK1) inhibitors. This dual readout assay can monitor both FP and TR-FRET signals from a single RSK1 kinase reaction by using the immobilized metal affinity for phosphochemical (IMAP)-based assay. The Z' value and signal to background (S/B) ratio were 0.85 and 4.0 using FP, and 0.79 and 10.6 using TR-FRET, which led to performance of a pilot library screening against the drug repositioning set consisting of 2320 compounds with a reasonable reproducibility. From this screening, we identified 16 compounds showing greater than 50% inhibition against RSK1 for both FP and TR-FRET; 6 compounds with greater than 50% inhibition only for FP; and 4 compounds with greater than 50% inhibition only for TR-FRET. In a cell-based functional assay to validate the hit compounds, 10 compounds identified only in a single assay had little effect on the RSK-mediated phosphorylation of liver kinase B1, whereas 5 compounds showing greater than 80% inhibition for both FP and TR-FRET reduced the phosphorylation of liver kinase B1. These results demonstrate that the dual readout assay can be used to identify hit compounds by subsequently monitoring both FP and TR-FRET signals from one RSK1 reaction.

Aberrant methylation of the VIM promoter in uterine cervical squamous cell carcinoma.

OBJECTIVES: To identify prognosis-associated methylation markers of uterine cervical squamous cell carcinoma (SCC) and to verify potential clinical correlations. METHODS: A genome-wide methylation array was performed using tissue samples of stage Ib1 (n = 9) and IIa (n = 5) tumors. Methylation levels were quantitatively evaluated by pyrosequencing for 54 tissue samples from SCC patients and 22 samples from normal controls. Clinicopathologic findings were obtained from medical records. Correlation or t test statistics were used to analyze the relationships between methylation levels and clinical features. Survival data were estimated using the Kaplan-Meier method and compared to the log-rank test. RESULTS: The methylation array identified 32 genes with distinct differences (p < 0.01) between stage Ib1 and IIa disease, and VIM was selected for further evaluation. Pyrosequencing analysis revealed that 40.7% of carcinoma samples had a higher methylation level in the VIM gene compared to the normal controls. VIM methylation status, low FIGO stage, and lack of parametrial involvement were significantly associated with longer disease-free survival (p = 0.036, p = 0.028, and p = 0.001, respectively). CONCLUSIONS: We profiled 32 genes that might be associated with prognosis in cervical cancer. We further revealed that the VIM gene is frequently methylated in cervical SCC and that its methylation might predict a favorable prognosis.

Disappearance of Serum Methylated p16 Indicates Longer Survival in Patients with Gastric Cancer.

PURPOSE: The aim of this study was to assess clinical correlations with postoperative alteration of p16 DNA methylation, and to clarify whether postoperative changes in the serum DNA methylation status of p16 could be used as a reliable prognostic factor for gastric cancer. MATERIALS AND METHODS: Fifty-three consecutive gastric adenocarcinoma patients who underwent gastric resection (Chung-Ang University Hospital, Seoul, Korea) were included. DNA methylation of p16 was evaluated by methylation-specific polymerase chain reaction using serum DNA preoperatively and at the 10th postoperative day. The correlation between changes in methylation status and patients' prognosis was analyzed. RESULTS: p16 was methylated in 79.2% of preoperative serum DNA and in 54.7% of postoperative serum DNA, respectively. Methylation in p16 disappeared more frequently in patients who underwent standard D2 lymphadenectomy compared to those who underwent modified D1+ lymphadenectomy (P=0.016). Whereas methylation of preoperative serum DNA was not correlated with survival, patients with postoperative disappearance of p16 methylation showed longer survival than those without postoperative disappearance of p16 methylation in the patients who had gastric cancer with lymph node metastasis (P=0.042). CONCLUSIONS: Postoperative disappearance of p16 methylation could be an available prognostic factor for node-positive gastric cancer.

Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer.

We tried to establish models that predict systemic recurrence in breast cancer by selecting marker clones with DNA copy number alterations (CNAs) using an array comparative genomic hybridization (CGH). Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess CNAs in 62 primary breast cancer tissues from 31 patients with systemic recurrence within 5 years after surgery and clinicopathologically well matched 31 patients who had no evidence of disease for at least 5years. Fourteen significant clones (11 clones showing gain and 3 showing loss) were identified by systemic recurrence-free survival (SRFS) analysis and 23 significant clones (17 clones showing gain and 6 showing loss) identified by chi(2) test and FDR test were selected as predictive markers of systemic breast cancer recurrence. The significant CNAs were found in the chromosomal regions of 5p15.33, 11q13.3, 15q26.3, 17q25.3, 18q23 and 21q22.3 with gain and 9p12, 11q24.1 and 14q32.33 with loss. We devised 2 prediction models for the systemic recurrence of breast cancer based on the 14 clones and the 23 clones, respectively. The survivals of the patients were significantly separated according to the scores from each model at the optimal cut off values in SRFS and overall survival analysis. We found candidate clones and genes of which CNAs were significantly associated with systemic recurrence of breast cancer. The devised prediction models with these clones were effective at differentiating the recurrence and nonrecurrence.

[The anaylsis of mortality rate according to CTP score and MELD score in patients with liver cirrhosis].

BACKGROUND/AIMS: The Model for End-Stage Liver Disease (MELD) consists of serum bilirubin and creatinine levels, International Normalized Ratio (INR) for prothrombin time, and etiology of liver disease. The MELD score is a reliable measurement of mortality risk and is suitable for a disease severity index in patients with end-stage liver disease. We examined the validity of the MELD as a disease severity index for patients with end-stage liver disease. METHODS: We investigated the 379 patients with liver cirrhosis hospitalized between January 1995 and May 2001. We retrospectively reviewed the hospital records to verify the diagnosis of cirrhosis and to collect exact patient information about their demographic data, portal hypertensive complications and laboratory data. The ability to classify patients with liver cirrhosis according to their risk of death was examined using the concordance c-statistic. RESULTS: The MELD score performed well in predicting death within 3 months with a c-statistic of 0.73 with etiology and 0.71 without etiology. The significant clinical, laboratory variables on 3 month survival in patients with liver cirrhosis are serum bilirubin, ascites and hepatic encephalopathy. The addition of portal hypertensive complications to the MELD score did not improve the accuracy of the MELD score. CONCLUSIONS: The MELD score is a useful disease severity index for the patients with end-stage liver disease and provides reliable measurement of short term survival over a wide range of liver disease severity and diverse etiology.