Biomedical subjects

Young-Gil Park

Publications and source records attributed to Young-Gil Park.

10 recordsLinked to original sources

PubMed2006

Differentiation of Mycobacterial species by hsp65 duplex PCR followed by duplex-PCR-based restriction analysis and direct sequencing.

Here we describe a novel duplex PCR method which can differentiate Mycobacterium tuberculosis and nontuberculosis mycobacteria (NTM) strains by amplifying hsp65 DNAs of different sizes (195 and 515 bp, respectively). The devised technique was applied to 54 reference and 170 clinical isolates and differentiated all strains into their respective groups with 100% sensitivity and specificity. Furthermore, a duplex PCR-restriction analysis (duplex PRA) and a direct sequencing protocol were developed to differentiate NTM strains at the species and subspecies levels based on previously reported hsp65 DNA sequences (H. Kim et al., Int. J. Syst. Evol. Microbiol. 55:1649-1656, 2005) and then applied to 105 NTM clinical isolates. All NTM isolates were clearly differentiated at the species and subspecies levels by subsequent procedures (PRA or direct sequencing) targeting 515-bp NTM duplex PCR amplicons. Our results suggest that novel duplex PCR-based methods are sensitive and specific for identifying mycobacterial culture isolates at the species level.

Bacterial Proteins↗

PubMed2005

Analysis of magnetization in nanocomposite Nd4.5(Fe,Cr)77B18.5 by electron holography and simulation.

Magnetization distribution in nanocomposite Nd4.5(Fe,Cr)77B18.5 was studied by electron holography and computer simulation. In order to understand the detailed magnetization distribution, the magnetic flux distribution was calculated taking into account the magnetic charge or the stray field on the basis of magnetization models consisting of small magnetic dipoles and was compared with that in reconstructed phase images experimentally observed. Through the comparison, the characteristic feature in the distribution of the magnetization distribution in the nanocomposite magnetic materials was clarified, and the distribution was found to well correspond to their magnetic properties. It is pointed out that for understanding magnetization, the interpretation of reconstructed phase images should be done through computer simulation just as the analysis of high-resolution electron microscope images. Eventually, it was demonstrated that electron holography with computer simulation is quite useful to analyze detailed magnetization distribution in nanocrystalline magnetic materials at the nanometer scale.

Journal Article↗

PubMed2005

PCR restriction fragment length polymorphism analysis (PRA)-algorithm targeting 644 bp Heat Shock Protein 65 (hsp65) gene for differentiation of Mycobacterium spp.

A method based on PCR-restriction fragment length polymorphism analysis (PRA) using a novel region of the hsp65 gene was developed for the rapid and exact identification of mycobacteria to the species level. A 644 bp region of hsp65 in 62 mycobacteria reference strains, and 4 related bacterial strains were amplified, and the amplified DNAs were subsequently digested with restriction enzymes, namely, AvaII, HphI, and HpaII. Most of the mycobacteria species were easily differentiated at the species level by the developed method. In particular, the method enabled the separation of M. avium, M. intracellulare and M. tuberculosis to the species level by AvaII digestion alone. An algorithm was constructed based on the results and a blind test was successfully performed on 251 clinical isolates, which had been characterized by conventional biochemical testing. Our results suggest that this novel PRA offers a simple, rapid, and accurate method for the identification of mycobacteria culture isolates at the species level.

Algorithms↗

PubMed2005

Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65).

The nucleotide sequences (604 bp) of partial heat-shock protein genes (hsp65) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an XhoI PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.

Bacterial Proteins↗

PubMed2004

Simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by polymerase chain reaction-single strand conformation polymorphism and sequence analysis of the RNA polymerase gene (rpoB).

Interspecies variations and mutations associated with rifampin resistance in rpoB of Mycobacterium allow for the simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by PCR-SSCP analysis and PCR- sequencing. One hundred and ten strains of rifampin-susceptible M. tuberculosis, 14 strains of rifampin-resistant M. tuberculosis, and four strains of the M. avium complex were easily identified by PCR-SSCP. Of another seven strains, which showed unique SSCP patterns, three were identified as rifampin-resistant M. tuberculosis and four as M. terrae complex by subsequent sequence analysis of their rpoB DNAs (306 bp). These results were concordant with those obtained by susceptibility testing, biochemical identification, and 16S rDNA sequencing.

Antitubercular Agents↗

PubMed2004

Identification of Mycobacterium tuberculosis by PCR-linked reverse hybridization using specific rpoB oligonucleotide probes.

A reverse probe hybridization method using two different Mycobacterium tuberculosis-specific rpoB DNA probes in combination was evaluated for the identification of M. tuberculosis culture isolates. Among the 384 isolates tested, 354 strains were identified as M. tuberculosis, which included 37 rifampin-resistant strains, and 30 were nontuberculous mycobacteria (NTM). This result was in accord with partial rpoB sequence analysis and IS6110 polymerase chain reaction (PCR) results, but not with the results of biochemical testing, which produced two false negative results. Because of its high level of sensitivity and specificity, we suggest that M. tuberculosis-specific rpoB probes immobilized on micro-titer well plates or on other solid matrixes can be used efficiently for the rapid and convenient identification of M. tuberculosis.

DNA Probes↗

PubMed2004

Electron holography on remanent magnetization distribution of melt-spun Nd-Fe-B magnets.

Microstructures and magnetic domain structures of melt-spun Nd-Fe-B permanent magnets were investigated in detail by analytical electron microscopy and electron holography. While the crystal orientation of matrix Nd2Fe14B grains was analyzed by nanobeam electron diffraction, precipitates of a few tens of nanometers at grain boundaries were identified to be alpha-Fe by energy-dispersive X-ray spectroscopy. The detailed magnetization distribution in Nd2Fe14B grains and at their boundaries was visualized by electron holography. Ex situ experimentation with an electromagnet revealed that the domain walls in the demagnetized state and remanent states were pinned at grain boundaries, and Fe precipitates at the grain boundary were situated at the center of the closure domain.

Boron↗

PubMed2004

Analytical electron microscopy and electron holography on microstructures and magnetic domain structures of Sm-Co 2:17 magnets.

Microstructures and magnetic domain structures of precipitation-hardened Sm-Co permanent magnets were systematically investigated by analytical electron microscopy and electron holography. By an elemental mapping method with energy-dispersive X-ray spectroscopy, the change in the local distribution of additive elements, i.e. Cu, Fe and Zr, in Sm-Co magnets with various heat treatments was visualized and the enrichment of Zr in the Z-phase with a width of approximately 1 nm was clarified directly. Detailed analysis with electron holography revealed that considerable fluctuation in the distribution of lines of magnetic flux in the step-aged magnet was due to the chemical partitioning of additives and resulted in magnetic hardening during the magnetization process.

Holography↗

PubMed2004

Transmission electron microscopy on thin film of high density magnetic composite prepared by FIB method.

A thin specimen of a high density magnetic composite (HDMC), which is a type of powder magnetic cores was prepared for transmission electron microscopy (TEM) using a focused ion beam (FIB) method. A homogeneous thin film containing an insulator boundary between the constituent Fe powders was obtained successfully. Using this thin film, detailed flow of magnetic flux was visualized by electron holography, and the magnetic flux density was estimated to be 1.73 +/- 0.09 T being consistent with that of a bulk HDMC (1.70 T). Moreover, through Lorentz microscopy, the characteristic magnetization process of HDMC was observed by applying the magnetic field up to approximately 8 kA/m.

Holography↗

PubMed2004

Differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria by duplex PCR assay using the RNA polymerase gene (rpoB).

A novel duplex PCR method that can amplify the 235- and 136-bp rpoB DNAs of Mycobacterium tuberculosis complex and nontuberculous mycobacteria (NTM), respectively, with two different sets of primers was used to differentially identify 44 reference strains and 379 clinical isolates of mycobacteria in a single-step assay. Showing 100% sensitivity and specificity, the duplex PCR method could clearly differentiate M. tuberculosis complex and NTM strains. In addition, restriction fragment length polymorphism analysis and direct sequencing of the amplicon of NTM could be used to supplement species identification.

Base Sequence↗