Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method.

PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina.

Prediction of a required log reduction with probability for Enterobacter sakazakii during high-pressure processing, using a survival/death interface model.

A probabilistic model for predicting Enterobacter sakazakii inactivation in trypticase soy broth (TSB) and infant formula (IF) by high-pressure processing was developed. The modeling procedure is based on a previous model (S. Koseki and K. Yamamoto, Int. J. Food Microbiol. 116:136-143, 2007) that describes the probability of death of bacteria. The model developed in this study consists of a total of 300 combinations of pressure (400, 450, 500, 550, or 600 MPa), pressure-holding time (1, 3, 5, 10, or 20 min), temperature (25 or 40 degrees C), inoculum level (3, 5, or 7 log(10) CFU/ml), and medium (TSB or IF), with each combination tested in triplicate. For each replicate response of E. sakazakii, survival and death were scored with values of 0 and 1, respectively. Data were fitted to a logistic regression model in which the medium was treated as a dummy variable. The model predicted that the required pressure-holding times at 500 MPa for a 5-log reduction in IF with 90% achievement probability were 26.3 and 7.9 min at 25 and 40 degrees C, respectively. The probabilities of achieving 5-log reductions in TSB and IF by treatment with 400 MPa at 25 degrees C for 10 min were 92 and 3%, respectively. The model enabled the identification of a minimum processing condition for a required log reduction, regardless of the underlying inactivation kinetics pattern. Simultaneously, the probability of an inactivation effect under the predicted processing condition was also provided by taking into account the environmental factors mentioned above.

Autocrine motility factor/glucose-6-phosphate isomerase is a possible predictor of metastasis in bone and soft tissue tumours.

In order to assess the involvement of autocrine motility factor (AMF) in mesenchymal tumours, AMF protein and mRNA expression was analysed in tumours, tumour-like lesions, and other lesions of bone and soft tissue. Immunohistochemical analysis of 200 cases revealed positive staining in 72.5% of the cases, suggesting that AMF is a widely expressed protein. Chordoid, chondroid, and muscular tumours revealed higher immunoreactivity in both benign and malignant tumours. Immunoblotting analysis corroborated the results of immunohistochemistry. Generally, malignant tumours revealed higher expression of AMF than benign tumours of the same histopathological lineage, except for dermatofibroma/dermatofibrosarcoma protuberans. However, mRNA levels were not concordant with protein levels, and sarcomas that displayed higher mRNA and lower protein expression levels showed a trend for distant metastasis. In cultured cells, AMF was secreted and detected in conditioned culture medium. Furthermore, when proteasome inhibitors were added to cells in order to examine the changes in turnover rates, these compounds did not significantly alter the intracellular levels of AMF protein. On the basis of these overall findings, it is suggested that a particular subset of sarcomas secrete AMF, rather than degrading this protein at a higher turnover rate. This secreted AMF presumably enhances their cell motility through an autocrine effect and eventually causes increased metastatic potential. Collectively, AMF was observed in a wide spectrum of lesions of mesenchymal tissue, supporting the notion that it is involved in various cellular functions, including proliferation, differentiation, metabolism, and metastasis. In addition, higher expression of its mRNA may indicate higher levels of protein secretion and define a particularly aggressive group of tumours with high metastatic potential.

Estrogen modulates ghrelin expression in the female rat stomach.

Ghrelin was recently identified as an endogenous ligand for GH secretagogue receptor. In this study, we investigated the effects of ovariectomy on the numbers of ghrelin-immunopositive and -expressing cells, ghrelin mRNA levels, and plasma ghrelin concentrations in 4- and 9-week-old female rats. Three days after ovariectomy, the number of ghrelin cells and plasma ghrelin level significantly increased in both 4- and 9-week-old rats and the ghrelin mRNA level also increased in 4-week-old rats. These responses were reversed by 17beta-estradiol replacement. We also found that ghrelin-immunopositive cells express estrogen receptor alpha. These results suggested that estrogen is involved in the regulation of ghrelin expression.

A composite hormone response element regulates transcription of the rat GHRH receptor gene.

To further elucidate the molecular mechanisms underlying the transcriptional regulation of the GHRH receptor (GHRH-R) gene, hormonal regulation of the promoter activity of this gene was examined. An approximately 3-kb genomic fragment spanning the promoter region of the gene was sequenced and the transcription start site was determined by RT-PCR and RNase protection assay. A major start site was localized at -105 (relative to the translation initiation codon, ATG), and a pit-1 binding sequence characteristic of pituitary specific genes was found at -155 to -146. Deletion and mutation studies demonstrated this site to be functional. In the presence of dexamethasone, the GHRH-R promoter (from -2935 to -11) directed luciferase expression in MtT-S cells, a somatotropic cell line, but not in the PC12 cells that normally do not express GHRH-R. While T(3), all trans-RA, and 9cis-RA alone weakly enhanced the reporter gene expression, each of these substances was found to act as a synergistic enhancer in the presence of dexamethasone. Additional deletion and mutation analyses demonstrated a functional RA response element at -1090 to -1074. Two functional glucocorticoid response elements and a T(3) response element were found in an 80-bp 5'-flanking sequence of the pit-1 site. Interestingly, it is suggested that the 6-bp half-site AGGACA (from -209 to -204) functions as a 3'-half-site of T(3) response element as well as a 5'-half-site of one of the glucocorticoid response elements.

Ghrelin-producing cells exist as two types of cells, closed- and opened-type cells, in the rat gastrointestinal tract.

Ghrelin was recently isolated from the rat stomach as an endogenous ligand for the growth-hormone secretagogue receptor (GHS-R) and is known to exist in the gastrointestinal tract and hypothalamus. In this study, we investigated in detail the distribution and morphologic characteristics of ghrelin-containing cells (ghrelin cells) in the gastrointestinal tract by immunohistochemistry and in situ hybridization. Ghrelin cells were found to be localized in the mucous membrane of the stomach, duodenum, ileum, cecum and colon but not in myenteric plexus, and they can be classified into open- and closed-type cells. The greatest number of ghrelin cells was found in the stomach, and it was found that the number of the opened-type cells gradually increased in the direction from stomach to the lower gastrointestinal tract. These results suggest that the two types of ghrelin cells may be distinctly regulated and play different physiological roles in various regions of the gastrointestinal tract.