OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults.

While some old adults stay healthy and non-frail up to late in life, others experience multimorbidity and frailty often accompanied by a pro-inflammatory state. The underlying molecular mechanisms for those differences are still obscure. Here, we used gene expression analysis to understand the molecular underpinning between non-frail and frail individuals in old age. Twenty-four adults (50% non-frail and 50% frail) from InCHIANTI study were included. Total RNA extracted from whole blood was analyzed by Cap Analysis of Gene Expression (CAGE). CAGE identified transcription start site (TSS) and active enhancer regions. We identified a set of differentially expressed (DE) TSS and enhancer between non-frail and frail and male and female participants. Several DE TSSs were annotated as lncRNA (XIST and TTTY14) and antisense RNAs (ZFX-AS1 and OVCH1 Antisense RNA 1). The promoter region chr6:366,786,54-366,787,97;+ was DE and overlapping the longevity CDKN1A gene. GWAS-LD enrichment analysis identifies overlapping LD-blocks with the DE regions with reported traits in GWAS catalog (isovolumetric relaxation time and urinary tract infection frequency). Furthermore, we used weighted gene co-expression network analysis (WGCNA) to identify changes of gene expression associated with clinical traits and identify key gene modules. We performed functional enrichment analysis of the gene modules with significant trait/module correlation. One gene module is showing a very distinct pattern in hub genes. Glycogen Phosphorylase L (PYGL) was the top ranked hub gene between non-frail and frail. We predicted transcription factor binding sites (TFBS) and motif activity. TF involved in age-related pathways (e.g., FOXO3 and MYC) shows different expression patterns between non-frail and frail participants. Expanding the study of OVCH1 Antisense RNA 1 and PYGL may help understand the mechanisms leading to loss of homeostasis that ultimately causes frailty.

AtCAST, a tool for exploring gene expression similarities among DNA microarray experiments using networks.

The comparison of gene expression profiles among DNA microarray experiments enables the identification of unknown relationships among experiments to uncover the underlying biological relationships. Despite the ongoing accumulation of data in public databases, detecting biological correlations among gene expression profiles from multiple laboratories on a large scale remains difficult. Here, we applied a module (sets of genes working in the same biological action)-based correlation analysis in combination with a network analysis to Arabidopsis data and developed a 'module-based correlation network' (MCN) which represents relationships among DNA microarray experiments on a large scale. We developed a Web-based data analysis tool, 'AtCAST' (Arabidopsis thaliana: DNA Microarray Correlation Analysis Tool), which enables browsing of an MCN or mining of users' microarray data by mapping the data into an MCN. AtCAST can help researchers to find novel connections among DNA microarray experiments, which in turn will help to build new hypotheses to uncover physiological mechanisms or gene functions in Arabidopsis.

Application of the improved BALB/c 3T3 cell transformation assay to the examination of the initiating and promoting activities of chemicals: the second interlaboratory collaborative study by the non-genotoxic carcinogen study group of Japan.

The Non-genotoxic Carcinogen Study Group in the Environmental Mutagen Society of Japan organised the second step of the inter-laboratory collaborative study on one-stage and two-stage cell transformation assays employing BALB/c 3T3 cells, with the objective of confirming whether the respective laboratories could independently produce results relevant to initiation or promotion. The method was modified to use a medium consisting of DMEM/F12 supplemented with 2% fetal bovine serum and a mixture of insulin, transferrin, ethanolamine and sodium selenite, at the stationary phase of cell growth. Seventeen laboratories collaborated in this study, and each chemical was tested by three to five laboratories. Comparison between the one-stage and two-stage assays revealed that the latter method would be beneficial in the screening of chemicals. In the test for initiating activity with the two-stage assay (post-treated with 0.1microg/ml 12-O-tetradecanoylphorbol-13-acetate), the relevant test laboratories all obtained positive results for benzo[a]pyrene and methylmethane sulphonate, and negative results for phenanthrene. Of those laboratories assigned phenacetin for the initiation phase, two returned positive results and two returned negative results, where the latter laboratories tested up to one dose lower than the maximum dose used by the former laboratories. In the exploration of promoting activity with the twostage assay (pretreated with 0.2microg/ml 3-methylcholanthrene), the relevant test laboratories obtained positive results for mezerein, sodium orthovanadate and TGF-beta1, and negative results for anthralin, phenacetin and phorbol. Two results returned for phorbol 12,13-didecanoate were positive, but one result was negative - again, the maximum dose to achieve the latter result was lower than that which produced the former results. These results suggest that this modified assay method is relevant, reproducible and transferable, provided that dosing issues, such as the determination of the maximum dose, are adequately considered. The application of this two-stage assay for screening the initiating and promoting potential of chemicals is recommended for consideration by other research groups and regulatory authorities.

[Examination of Staphylococcus aureus survival and growth during cheese-making process].

Inoculation tests of Staphylococcus aureus were performed to evaluate the risk of toxic hazard in cheese manufacturing processes. S. aureus was inoculated into pasteurized milk or cheese curd, and the survival and growth were examined. S. aureus grew only slightly or decreased in cell number under the manufacturing condition of semi-hard type cheese or soft-type cheese. Under the conditions of the fresh cheese making process, S. aureus slightly increased in cell number, though no enterotoxin was detected. In processed cheese, S. aureus did not grow at all. Growth inhibition of S. aureus by lactic acid produced from starter culture was suggested to be the cause of growth inhibition in the natural cheese.