Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics.

Completion of human genome sequencing has greatly accelerated functional genomic research. Full-length cDNA clones are essential experimental tools for functional analysis of human genes. In one of the projects of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, the full-length human cDNA sequencing project (FLJ project), nucleotide sequences of approximately 30 000 human cDNA clones have been analyzed.

Calcification by MC3T3-E1 cells on RGD peptide immobilized on titanium through electrodeposited PEG.

The effect of a cell-adhesive peptide containing Arg-Gly-Asp (RGD) immobilized through poly(ethylene glycol) (PEG) on titanium (Ti) on calcification by MC3T3-E1 cells was investigated to develop a new surface modification technique using biofunctional molecules. RGD was immobilized on Ti through PEG, both terminals of which were terminated with -NH(2) and -COOH to combine with the Ti surface and RGD. PEG was immobilized on Ti with electrodeposition, and RGD, with immersion.

Human protein factory for converting the transcriptome into an in vitro-expressed proteome,

Appropriate resources and expression technology necessary for human proteomics on a whole-proteome scale are being developed. We prepared a foundation for simple and efficient production of human proteins using the versatile Gateway vector system. We generated 33,275 human Gateway entry clones for protein synthesis, developed mRNA expression protocols for them and improved the wheat germ cell-free protein synthesis system.

PB2 protein of a highly pathogenic avian influenza virus strain A/chicken/Yamaguchi/7/2004 (H5N1) determines its replication potential in pigs.

It has been shown that not all but most of the avian influenza viruses replicate in the upper respiratory tract of pigs (H. Kida et al., J.

Effect of pH on the interaction between zwitterions and titanium oxide.

The isoelectric points (IEPs) of two zwitterions, glycine and both-terminals-terminated poly(ethylene glycol) (NH(2)-PEG-COOH), were determined from the titration curves, and the thicknesses of zwitterion layers immobilized on titanium (Ti) with immersion and electrodeposition at various pH based on IEPs were evaluated with ellipsometry to investigate the effect of pH and the immobilization technique on the interactions between the zwitterions and the Ti surface. From the titration curves, pK(1), pK(2), and the IEP of glycine were determined as 2.8, 8.

Induction of the differentiation of human HL-60 promyelocytic leukemia cell line by succinoyl trehalose lipids.

Four analogs of succinoyl trehalose lipid-3 (STL-3)with saturated even-number or odd-number carbonchains, and unsaturated or halogenated fatty acidswere examined for their ability to inhibit the growthand induce the differentiation of HL-60 humanpromyelocytic leukemia cells. The optimalconcentration of STL-3 at which such activities wererecognized was closed to the critical micelleconcentration of STL-3. Analog of STL-3 witheven-number or odd-number carbon chain and unsaturatedfatty acids strongly inhibited growth and induced thedifferentiation of HL-60 cells, as evaluated in termsof nitroblue tetrazilium-reducing activity and theappearance of the CD36 antigen.

Mannosylerythritol lipid increases levels of galactoceramide in and neurite outgrowth from PC12 pheochromocytoma cells.

We report here that a microbial extracellular glycolipid,mannosylerythritol lipid (MEL), induces the outgrowth ofneurites from and enhances the activity of acetylcholinesterase(AChE) in PC12 pheochromocytoma cells. Furthermore, treatment ofPC12 cells with MEL increased levels of galactosylceramide(Galbeta1-1'Cer; GalCer). Exposure of PC12 cells to exogenous GalCer caused the dose-dependent outgrowth ofneurites.

Treatment of mouse melanoma cells with phorbol 12-myristate 13-acetate counteracts mannosylerythritol lipid-induced growth arrest and apoptosis.

Mannosylerythritol lipid (MEL), an extracellularglycolipid from yeast, induces the differentiation ofHL-60 promyelocytic leukemia cells towardsgranulocytes. We show here that MEL is also a potentinhibitor of the proliferation of mouse melanoma B16cells. Flow-cytometric analysis of the cell cycle ofMEL-treated B16 cells revealed the accumulation ofcells in the sub-G(0)/G(1) phase, which is a hallmark ofcells undergoing apoptosis.

Biofilm formation by lactic acid bacteria and resistance to environmental stress.

We investigated the formation of biofilms by 3 type strains of lactic acid bacteria (LAB), Lactobacillus plantarum, Lactobacillus brevis and Lactobacillus fructivorans, as representatives of LAB that cause food deterioration or contamination. Lactobacillus plantarum subsp. plantarum JCM1149 and Lactobacillus brevis JCM1059 appeared to adhere and accumulate on glass cover slips.

Diversity and similarity of microbial communities in petroleum crude oils produced in Asia.

To understand microbial communities in petroleum crude oils, we precipitated DNA using high concentrations of 2,2,4-trimethylpentane (isooctane) and purified. Samples of DNA from five crude oils, (Middle East, 3; China, 1; and Japan, 1) were characterized based upon their 16S rRNA gene sequences after PCR amplification and the construction of clone libraries. We detected 48 eubacterial species, one cyanobacterium, and one archaeon in total.

Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.

The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea and in eukarya, by LAGLIDADG and His-Cys box homing endonucleases, respectively.

Natural human interferon beta plus ribavirin combination therapy in Japanese patients infected with hepatitis C virus and a high viral load.

Objective: The aim of this pilot study was to determine the safety and efficacy of natural human interferon beta (nIFNbeta) plus ribavirin (RBV) in patients with chronic hepatitis C who did not respond to pegylated interferon alpha (PEG-IFN), with special emphasis on the incidence of mental disorders or refusal for fear of adverse effects.

Methods: We studied 19 patients with HCV genotype 1b, 2a or 2b and a high viral load, including 8 patients with mental disorders. They were treated with nIFNbeta-RBV.

Influence of the Pseudomonas quinolone signal on denitrification in Pseudomonas aeruginosa.

Denitrification is a well-studied respiratory system that is also important in the biogeochemical nitrogen cycle. Environmental signals such as oxygen and N-oxides have been demonstrated to regulate denitrification, though how denitrification is regulated in a bacterial community remains obscure. Pseudomonas aeruginosa is a ubiquitous bacterium that controls numerous genes through cell-to-cell signals.

An aneurysm at the cannulation site discovered 40 years after cardiac surgery: report of a case.

We report the successful surgical treatment of a pseudoaneurysm of the ascending aorta in a 45-year-old man who underwent surgical closure of a ventricular septal defect at the age of 5. A computed tomography scan ordered for the investigation of a pulmonary mass happened to detect a pseudoaneurysm (20 mm diameter). The pseudoaneurysm protruded anteriorly from the ascending aorta at the previous aortic cannulation site.

Rac1 mediates phorbol 12-myristate 13-acetate-induced migration of glioblastoma cells via paxillin.

Previously, we reported that phorbol 12-myristate 13-acetate (PMA)-activated protein kinase C (PKC) induced Rac1 activation in A172 glioblastoma cells. In this study, we investigated the mechanism of PMA-activated PKC-induced migration of glioblastoma cells by focusing on Rac1. PMA-induced formation of lamellipodia and focal complexes following migration were blocked by inhibiting Rac1 with small interfering RNA (siRNA), implicating Rac1 in PMA-induced glioblastoma cell migration.

Application of quantitative gene expression analysis for pertussis vaccine safety control.

Although vaccines are routinely used to prevent infectious diseases, little is known about the comprehensive influences caused by vaccines. In this study, we showed, using comprehensive gene expression analysis, that pertussis vaccine affected many genes in multiple organs of vaccine-treated animals. In particular, lung was revealed to be the most suitable target to evaluate pertussis vaccine toxicity.

Development of a novel biofilm continuous culture method for simultaneous assessment of architecture and gaseous metabolite production.

The way that gaseous metabolite production changes along with biofilm architecture development is poorly understood. To address this question, we developed a novel flow reactor biofilm culture method that allows for simultaneous assessment of gaseous metabolite production and architecture visualization. In this report, we establish the utility of this method using denitrification by Pseudomonas aeruginosa biofilms as a model system.

Molecular analysis of hypoxanthine guanine phosphoribosyltransferase (HPRT) deficiencies: novel mutations and the spectrum of Japanese mutations.

Inherited mutation of hypoxanthine guanine phosphoribosyltransferase, (HPRT) gives rise to Lesch-Nyhan syndrome or HPRT-related gout. We have identified a number of HPRT mutations in patients manifesting different clinical phenotypes, by analyzing all nine exons of the HPRT gene (HPRT1) from genomic DNA and reverse transcribed mRNA using the PCR technique coupled with direct sequencing. Recently, we detected two novel mutations: a single nucleotide substitution (430C > T) resulting in a nonsense mutation Q144X, and a deletion of HPRT1 exon 1 expressing no mRNA of HPRT.

Considerations for intravascular administration of oncolytic herpes virus for the treatment of multiple liver metastases.

Purpose: Oncolytic viral therapy is a newly developed modality for treating tumors. Many clinical trials using oncolytic virus have been performed worldwide, but most of them have used local injection in the tumor. Determination of the effect and safety of intravascular virus injection instead of local injection is necessary for clinical use against multiple liver metastases and systemic metastases.

Advanced method for high-throughput expression of mutated eukaryotic membrane proteins in Saccharomyces cerevisiae.

Crystallization of eukaryotic membrane proteins is a challenging, iterative process. The protein of interest is often modified in an attempt to improve crystallization and diffraction results. To accelerate this process, we took advantage of a GFP-fusion yeast expression system that uses PCR to direct homologous recombination and gene cloning.

Clinical and immunological evaluation of anti-apoptosis protein, survivin-derived peptide vaccine in phase I clinical study for patients with advanced or recurrent breast cancer.

Background: We previously reported that survivin-2B, a splicing variant of survivin, was expressed in various types of tumors and that survivin-2B peptide might serve as a potent immunogenic cancer vaccine. The objective of this study was to examine the toxicity of and to clinically and immunologically evaluate survivin-2B peptide in a phase I clinical study for patients with advanced or recurrent breast cancer.

Methods: We set up two protocols.

Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome.

Many poly(lactic acid) (PLA)-degrading microorganisms have been isolated from the natural environment by culture-based methods, but there is no study about unculturable PLA-degrading microorganisms. In this study, we constructed a metagenomic library consisting of the DNA extracted from PLA disks buried in compost. We identified three PLA-degrading genes encoding lipase or hydrolase.

A practical device for pinpoint delivery of molecules into multiple neurons in culture.

We have developed a device for pinpoint delivery of chemicals, proteins, and nucleic acids into cultured cells. The principle underlying the technique is the flow of molecules from the culture medium into cells through a rupture in the plasma membrane made by a needle puncture. DNA transfection is achieved by stabbing the needle tip into the nucleus.

Opr86 is essential for viability and is a potential candidate for a protective antigen against biofilm formation by Pseudomonas aeruginosa.

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that is one of the most refractory to therapy when it forms biofilms in the airways of cystic fibrosis patients. To date, studies regarding the production of an immunogenic and protective antigen to inhibit biofilm formation by P. aeruginosa have been superficial.

Application of DNA microarray technology to influenza A/Vietnam/1194/2004 (H5N1) vaccine safety evaluation.

We propose that DNA microarray analysis can be used in the quality control of pandemic and endemic influenza vaccine. Based on the expression profiles of 76 genes in the rat lung one day after inoculation of influenza vaccine, we can distinguish whole-virion influenza vaccine (PDv: pandemic influenza vaccine and WPv: whole virion-particle vaccine) and sub-virion vaccine (HA vaccine) from saline. Among these 76 genes, we found genes up-regulated by influenza infection, as well as genes involved in the immune response, and interferon.