Effective procedure to develop alternative annotations of bacterial tRNA genes by means of deductive inference on the basis of characteristic tandems of tRNA genes

In a series of analysis of genomic DNA sequences, we have established an induction-deduction method to dig up hidden tRNA and rRNA genes from bacterial genome DNA sequences by means of a concept of a characteristic tRNA-gene tandem we have ldeveloped, and are accumulating information on positions of putative tRNA and rRNA genes to be proposed as alternative annotations to the DDBJ/GenBank/EMBL Database. We have searched the DNA sequences near the existing tRNA genes as golcondas for tRNA genes, and found mord than fifty genes, e.g. tRNA-Ser and tRNA-Met in [AB013377], and 5S rRNAs in [AE014192], [AE017000], and others. A part of miserable states of the Database was partly introduced, and it is discussd how such status will be disso1ved. In addition, we proposed some ideas to maintain and improve the DDBJ/GenBank/EMBL database

Sensitive determination of total particulate phosphorus and particulate inorganic phosphorus in seawater using liquid waveguide spectrophotometry

Determining the total particulate phosphorus (TPP) and particulate inorganic phosphorus (PIP) in oligotrophic oceanic water generally requires the filtration of a large amount of water sample. This paper describes methods that require small filtration volumes for determining the TPP and PIP concentrations. The methods were devised by validating or improving conventional sample processing and by applying highly sensitive liquid waveguide spectrophotometry to the measurements of oxidized or acid-extracted phosphate from TPP and PIP, respectively. The oxidation of TPP was performed by a chemical wet oxidation method using 3% potassium persulfate. The acid extraction of PIP was initially carried out based on the conventional extraction methodology, which requires 1 M HCl, followed by the procedure for decreasing acidity. While the conventional procedure for acid removal requires a ten-fold dilution of the 1 M HCl extract with purified water, the improved procedure proposed in this study uses 8 M NaOH solution for neutralizing 1 M HCl extract in order to reduce the dilution effect. An experiment for comparing the absorbances of the phosphate standard dissolved in 0.1 M HCl and of that dissolved in a neutralized solution [1 M HCl : 8 M NaOH = 8:1 (v:v)] exhibited a higher absorbance in the neutralized solution. This indicated that the improved procedure completely removed the acid effect, which reduces the sensitivity of the phosphate measurement. Application to an ultraoligotrophic water sample showed that the TPP concentration in a 1075 mL-filtered sample was 8.4 nM with a coefficient of variation (CV) of 4.3% and the PIP concentration in a 2300 mL-filtered sample was 1.3 nM with a CV of 6.1%. Based on the detection limit (3 nM) of the sensitive phosphate measurement and the ambient TPP and PIP concentrations of the ultraoligotrophic water, the minimum filtration volumes required for the detection of TPP and PIP were estimated to be 15 and 52 mL, respectively

BORTEZOMIB-ENHANCED RADIOSENSITIZATION IN HUMAN ORAL CANCER CELLS

Oral cancer cells have a significantly augmented nuclear factor-κB (NF-κB) activity and the inhibition of this activity suppresses tumor growth. Bortezomib is a proteasome inhibitor and a drug used for molecular-targeted therapy (targets NF-κB). In this study, we investigated whether bortezomib would be effective as an inhibitor of proliferation and a radiosensitizer for the treatment of oral cancer. We demonstrate that bortezomib inhibits NF-κB activity and cell proliferation. The combined treatment with bortezomib and radiation (RT) suppressed NF-κB activity and cell growth in vitro and in vivo compared with RT treatment alone. To investigate the mechanisms by which bortezomib suppresses tumor growth, the expression of signaling molecules downstream of NF-κB were examined by ELISA. The combined treatment significantly inhibited the radiation‑induced production of angiogenic factors and decreased the number of blood vessels in the tumor tissues. Although the expression of anti‑apoptotic proteins was upregulated by RT, bortezomib downregulated the RT-induced expression of these proteins. Moreover, the expression of cleaved poly(ADP‑ribose) polymerase in vitro and in vivo was enhanced by bortezomib, indicating that bortezomib inhibits tumor growth by inducing apoptosis. This study clearly demonstrates that bortezomib significantly inhibits tumor growth and that the combined treatment with bortezomib and RT results in a significant inhibition of tumor growth. The mechanisms underlying the inhibition of tumor growth by bortezomib include the suppression of angiogenesis and the induction of apoptosis. A novel molecular targeting therapy including bortezomib may be effective in the treatment of oral cancer by suppressing NF-κB activity

Role of miR-518c-5p in Oral Cancer

We have previously demonstrated that a stromal cell-derived factor-1 (SDF-1; CXCL12)/CXCR4 system is involved in the establishment of metastasis in oral cancer. Recently, small non coding RNAs, microRNAs (miRNAs) have been shown to be involved in the metastatic process of several types of cancers. However, the miRNAs that contribute to metastases induced by the SDF-1/CXCR4 system in oral cancer are largely unknown. In this study, we examined the metastasis-related miRNAs induced by the SDF-1/CXCR4 system using B88-SDF-1 oral cancer cells, which exhibit functional CXCR4 and distant metastatic potential in vivo. Through miRNA microarray analysis, we identified the upregulation of miR-518c-5p in B88- SDF-1 cells, and confirmed the induction by real-time PCR analysis. Although an LNA-based miR-518c-5p inhibitor did not affect cell growth of B88-SDF-1 cells, it did significantly inhibit the migration of the cells. Next, we transfected a miR-518c expression vector into parental B88 cells and CAL27 oral cancer cells and isolated stable transfectants, B88-518c and CAL27-518c cells, respectively. The anchorage-dependent and -independent growth of miR-518c transfectants was significantly enhanced compared with the growth of mock cells. Moreover, we detected the enhanced migration of these cells. The LNA-based miR-518c-5p inhibitor significantly impaired the enhanced cell growth and migration of miR-518c transfectants, indicating that these phenomena were mainly dependent on the expression of miR-518c-5p. Next, we examined the function of miR-518c-5p in vivo. miR-518c transfectants or mock transfectants were inoculated into the masseter muscle or the blood vessels of nude mice. Tumor volume, lymph nodes metastasis, and lung metastasis were significantly increased in the mice inoculated with the miR-518c transfectants. These results indicated that miR-518c-5p regulates the growth and metastasis of oral cancer as a downstream target of the SDF-1/CXCR4 system

ANTI-TUMOR EFFICACY OF DOCETAXEL AND 5-FLUOROURACIL

Docetaxel (DOC) and 5-fluorouracil (5-FU) are important anticancer agents widely used in the treatment of a variety of cancers including oral squamous cell carcinoma (OSCC). The purpose of this study was to determine the antitumor efficacy of the sequential administration of DOC and 5-FU against OSCC cells (B88 and CAL27 cells) in vitro and in vivo. In in vitro growth inhibition assays, sequential treatment with DOC followed by 5-FU was more effective in inhibiting cancer cell growth than 5-FU followed by DOC, single treatment with DOC or 5-FU, or combined treatment with DOC and 5-FU. Furthermore, DOC followed by 5-FU significantly inhibited tumor growth in vivo compared to 5-FU followed by DOC. To understand the mechanisms underlying the enhanced growth inhibitory effect of the administration sequence, DOC followed by 5-FU, we examined the expression of 5-FU metabolic enzymes such as thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD) and orotate phosphoribosyl transferase (OPRT), which were known to regulate the antitumor effect of 5-FU, by real-time RT-PCR and western blot analysis. Downregulation of TS and DPD expression and upregulation of OPRT expression were induced by DOC treatment, suggesting that DOC enhanced the efficacy of 5-FU by altering the expression of its metabolic enzymes. These results indicate that sequential treatment with DOC followed by 5-FU could be a promising therapeutic strategy for oral cancer

tRNADB-CE: tRNA gene database curated manually by experts

We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and approximately 6.2 million DNA fragment sequences obtained from metagenomic analyses. This exhaustive search for tRNA genes was performed by running three computer programs to enhance completeness and accuracy of the prediction. Discordances of assignment among three programs were found for ∼4% of the total of tRNA gene candidates obtained from these prokaryote genomes analyzed. The discordant cases were manually checked by experts in the tRNA experimental field. In total, 144 061 tRNA genes were registered in the database ‘tRNADB-CE’, and the number of the genes was more than four times of that of the genes previously reported by the database from analyses of complete genomes with tRNAscan-SE program. The tRNADB-CE allows for browsing sequence information, cloverleaf structures and results of similarity searches among all tRNA genes. For each of the complete genomes, the number of tRNA genes for individual anticodons and the codon usage frequency in all protein genes and the positioning of individual tRNA genes in each genome can be browsed. tRNADB-CE can be accessed freely at http://trna.nagahama-i-bio.ac.jp

トクシマシ イシカイ ノ トウニョウビョウ タイサク

Tokushima City Medical Association has founded the committee for the means to prevent diabetesmellitus, because the mortality rate by diabetes mellitus in Tokushima Prefecture remainedranked first for 14 years from 1993 to 2006. It has enlightened a large number of people, such asdiabetic patients and candidates for diabetes, and also healthy citizens in Tokushima for preventingdiabetes mellitus. For this aim, Tokushima City Medical Association has made the home pagenamed Tokushima City Diabetic Network to show clearly the means to prevent diabetes mellitusfor the citizens. By this Web site, the citizens can get a correct knowledge about diabetes mellitus,a useful information about the treatments including exercises, diets and medications, and an informationabout medical institutions by utilizing the search page to receive a proper diabetic treatment.Tokushima City Medical Association held several events, such as Tokushima citizens’extension courses and diabetes forums for the citizens to understand diabetes mellitus clearly.Fortunately, in 2007, Tokushima got out of the first rank of diabetic mortality rate. TokushimaCity Medical Association will continue efforts to prevent diabetes mellitus by approaching the citizensof all ages from various aspects