Biomedical subjects

Tae Kwang Oh

Publications and source records attributed to Tae Kwang Oh.

7 recordsLinked to original sources

PubMed2006

Towards pathogenomics: a web-based resource for pathogenicity islands.

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at http://www.gem.re.kr/paidb.

Bacteria↗

PubMed2005

Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent.

Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we present the 7.2-megabase genome of the marine bacterium Hahella chejuensis including genes responsible for the biosynthesis of a pigment which has the lytic activity against a red-tide dinoflagellate. H.chejuensis is the first sequenced species in the Oceanospiralles clade, and sequence analysis revealed its distant relationship to the Pseudomonas group. The genome was well equipped with genes for basic metabolic capabilities and contained a large number of genes involved in regulation or transport as well as with characteristics as a marine heterotroph. Sequence analysis also revealed a multitude of genes of functional equivalence or of possible foreign origin. Functions encoded in the genomic islands include biosynthesis of exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigmentation. Molecular structure of the algicidal pigment, which was determined through LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In conclusion, our work provides new insights into mitigating algal blooms in addition to genetic make-up, physiology, biotic interactions and biological roles in the community of a marine bacterium.

Adaptation, Physiological↗

PubMed2005

A computational approach for identifying pathogenicity islands in prokaryotic genomes.

BACKGROUND: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. RESULTS: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs. CONCLUSION: Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.

Bacteria↗

PubMed2005

Enhancement of natural pigment extraction using Bacillus species xylanase.

Pigment extracts from the root of Lithospermum erythrorhizon are used as natural red dyes, as well as basic drugs due to their numerous pharmacological activities. In recent years, the demand for such natural pigment materials has increased; however, in natural dye production, the pigment yield is strongly affected by the source of cultivation, extracting conditions, and solvents. Accordingly, this study proposes a method of enzymatic pigment production based on the introduction of hydrolytic enzymes prior to the usual extraction to avoid repeated pigment extraction. The matrix destruction in the epidermal layer of the root by the enzymes was found to improve the pigment extractability, that is, the increment of K(L), the mass transfer coefficient, representing the pigment mobility in the epidermal layer. The root tissue maceration by the hydrolytic enzymes was also measured to evaluate the pigment extractability, and a linear relationship was observed between the K(L) values and the tissue maceration up to the addition of 3000 units/g of xylanase, indicating that the enzymatic maceration proportionally increases the interfacial area between the pigment and the solvent. Bacillus sp. DX107 xylanase only served to increase the extractability of the pigment by loosening the root shell matrix, without affecting the contents and color properties of the pigment, as almost no difference was found in the color between the pigments extracted using xylanase and those extracted according to the traditional method.

Bacillus↗

PubMed2005

Identification of flavonoids using liquid chromatography with electrospray ionization and ion trap tandem mass spectrometry with an MS/MS library.

Searchable MS/MS spectra libraries, constructed using the results of liquid chromatography coupled with electrospray ionization (ESI) tandem mass spectrometry (LC/MS/MS) with data-dependent acquisition on an ion trap mass spectrometer, are presented with regard to the identification and confirmation of a variety of closely related flavonoids in a set of biological samples. Flavonoids were found to exhibit a maximum amount of structurally specific MS/MS spectra at 45% of normalized collision energy on the instrument used, without wideband activation. These MS/MS spectra were then searched automatically against a 297-substance MS/MS library that contains many previously acquired spectra of standard flavonoids. The possible applications of this powerful technique to biological samples are also discussed. Daidzein and genistein were identified through the MS/MS spectra library while searching through LC/MS/MS data for plant and microbial extracts. Moreover, these compounds proved completely distinguishable from other flavonoids of closely related structures in the MS/MS spectra library, using the NIST MS search program. The applicability of the library-searchable spectra at low concentrations was demonstrated by successful identification of daidzein and genistein at 0.05 and 0.5 microg/mL, respectively.

Chromatography, High Pressure Liquid↗

PubMed2004

Enhancement of tyrosinase inhibition of the extract of Veratrum patulum using cellulase.

Inhibitors of melanin biosynthesis were screened by using three different methods. The extract of Veratrum patulum contains hydroxystilbene compounds that are potent tyrosinase inhibitors. We evaluated the enzyme inhibitory property on the mushroom tyrosinase of hydroxystilbene compounds including resveratrol, oxyresveratrol, and their analogs. Biotransformation using cellulase of the whole extract brought about an increase in the inhibitory activity of the products on mushroom tyrosinase. The enhancement of tyrosinase inhibition is supposed to increase the concentration of aglycon, which has superior inhibitory activity to its glycoside. Eventually, melanin biosynthesis was inhibited by the enhanced tyrosinase inhibitory activity of the extract. This result indicated that deglycosylation of stilbene compounds has exerted more effective inhibition on the enzyme than that of the unprocessed plant extract.

Agaricales↗

PubMed2002

Expression and characterization of Ca(2+)-independent lipase from Bacillus pumilus B26.

A lipase-producing Bacillus pumilus strain (B26) was isolated from a soil sample collected in Korea. The cloned gene showed that the lipase B26 composed of a 34-amino-acid signal sequence and a 181-amino-acid mature part corresponding to a molecular mass (M(r)) of 19,225. Based on the M(r) and the protein sequence, the lipase B26 belongs to the lipase family I.4. The optimum temperature and pH of the purified enzyme were 35 degrees C and 8.5, respectively. The lipase B26 showed a 'Ca(2+)-independent thermostability and catalytic activity'. These are novel properties observed for the first time in lipase B26 among all bacterial lipases and correspond with the suggestion that this enzyme had no Ca(2+)-binding motif around the catalytic His156 residue. This enzyme seems to be a true lipase based on the experimental results that it could hydrolyze various long-chain triglycerides (C(14)-C(18)) and triolein (C(18:1)) and that it showed a typical interfacial activation mechanism toward both tripropionin and p-nitrophenyl butyrate.

Amino Acid Sequence↗