Biomedical subjects

Yoichi Murakami

Publications and source records attributed to Yoichi Murakami.

4 recordsLinked to original sources

PubMed2006

SHARP2: protein-protein interaction predictions using patch analysis.

UNLABELLED: SHARP2 is a flexible web-based bioinformatics tool for predicting potential protein-protein interaction sites on protein structures. It implements a predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. Six parameters are calculated: solvation potential, hydrophobicity, accessible surface area, residue interface propensity, planarity and protrusion (SHARP2). Parameter scores for each patch are combined, and the patch with the highest combined score is predicted as a potential interaction site. SHARP2 enables users to upload 3D protein structure files in PDB format, to obtain information on potential interaction sites as downloadable HTML tables and to view the location of the sites on the 3D structure using Jmol. The server allows for the input of multiple structures and multiple combinations of parameters. Therefore predictions can be made for complete datasets, as well as individual structures. AVAILABILITY: http://www.bioinformatics.sussex.ac.uk/SHARP2.

Algorithms↗

PubMed2005

Polarization dependence of the optical absorption of single-walled carbon nanotubes.

Anisotropic optical absorption properties of single-walled carbon nanotubes (SWNTs) are determined from a vertically aligned SWNT film for 0.5-6 eV. Absorption peaks at 4.5 and 5.25 eV are found to exhibit remarkable polarization dependence and have relevance to optical properties of graphite. A method for determining a nematic order parameter for an aligned SWNT film based on the collinear absorption peak at 4.5 eV is presented, followed by the determination of the optical absorption cross section.

Journal Article↗

PubMed2004

Generation of single-walled carbon nanotubes from alcohol and generation mechanism by molecular dynamics simulations.

Recent advances in high-purity and high-yield catalytic chemical vapor deposition (CVD) generation of single-walled carbon nanotubes (SWNTs) from alcohol are comprehensively presented and discussed on the basis of results obtained from both experimental and numerical investigations. We have uniquely adopted alcohol as a carbon feedstock, and this has resulted in high-quality, low-temperature synthesis of SWNTs. This technique can produce SWNTs even at a very low temperature of 550 degrees C, which is about 300 degrees C lower than the conventional CVD methods in which methane or acetylene is typically used. We demonstrate the excellence of the proposed alcohol catalytic CVD method for high-yield production of SWNTs when Fe-Co on USY-zeolite powder was used as a catalyst. At optimum CVD conditions, a SWNT yield of more than 40 wt % was achieved over the weight of the catalytic powder within the reaction time of 120 min. In addition to the advantages for mass production, this method is also suitable for the direct synthesis of high-quality SWNTs on Si and quartz substrates when combined with the newly developed liquid-based "dip-coat" technique to mount catalytic metals on the surface of substrates. This method allows easy and costless loading of catalytic metals without the need for any support or underlayer materials that were usually required in previous studies for the generation of a sufficient quantity of SWNTs on an Si surface. Finally, the result of molecular dynamics simulation for the SWNT growth process is presented to obtain a fundamental insight into the initial growth mechanism on the catalytic particles.

Alcohols↗

PubMed2003

In vitro and in vivo antibacterial activities of DK-507k, a novel fluoroquinolone.

The antibacterial activities of DK-507k, a novel quinolone, were compared with those of other quinolones: ciprofloxacin, gatifloxacin, levofloxacin, moxifloxacin, sitafloxacin, and garenoxacin (BMS284756). DK-507k was as active as sitafloxacin and was as active as or up to eightfold more active than gatifloxacin, moxifloxacin, and garenoxacin against Streptococcus pneumoniae, methicillin-susceptible and methicillin-resistant Staphylococcus aureus, and coagulase-negative staphylococci. DK-507k was as active as or 4-fold more active than garenoxacin and 2- to 16-fold more active than gatifloxacin and moxifloxacin against ciprofloxacin-resistant strains of S. pneumoniae, including clinical isolates and in vitro-selected mutants with known mutations. DK-507k inhibited all ciprofloxacin-resistant strains of S. pneumoniae at 1 microg/ml. A time-kill assay with S. pneumoniae showed that DK-507k was more bactericidal than gatifloxacin and moxifloxacin. The activities of DK-507k against most members of the family Enterobacteriaceae were comparable to those of ciprofloxacin and equal to or up to 32-fold higher than those of gatifloxacin, levofloxacin, moxifloxacin, and garenoxacin. DK-507k was fourfold less active than sitafloxacin and ciprofloxacin against Pseudomonas aeruginosa, while it was two to four times more potent than levofloxacin, gatifloxacin, moxifloxacin, and garenoxacin against P. aeruginosa. In vivo, intravenous treatment with DK-507k was more effective than that with gatifloxacin and moxifloxacin against systemic infections caused by S. aureus, S. pneumoniae, and P. aeruginosa in mice. In a mouse model of pneumonia due to penicillin-resistant S. pneumoniae, DK-507k administered subcutaneously showed dose-dependent efficacy and eliminated the bacteria from the lungs, whereas gatifloxacin and moxifloxacin had no significant efficacy. Oral treatment with DK-507k was slightly more effective than that with ciprofloxacin in a rat model of foreign body-associated urinary tract infection caused by a P. aeruginosa isolate for which the MIC of DK-507k was fourfold higher than that of ciprofloxacin. Oral administration of DK-507k to rats achieved higher peak concentrations in serum and higher concentrations in cumulative urine than those achieved with ciprofloxacin. These data indicate the potential advantages of DK-507k over other quinolones for the treatment of a wide range of community-acquired infections.

Animals↗