Biomedical subjects

Jin-A Kim

Publications and source records attributed to Jin-A Kim.

11 recordsLinked to original sources

PubMed2006

Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives.

We have newly identified five Terminal-repeat retrotransposon in miniature (TRIM) families, four from Brassica and one from Arabidopsis. A total of 146 elements, including three Arabidopsis families reported before, are extracted from genomics data of Brassica and Arabidopsis, and these are grouped into eight distinct lineages, Br1 to Br4 derived from Brassica and At1 to At4 derived from Arabidopsis. Based on the occurrence of TRIM elements in 434 Mb of B. oleracea shotgun sequences and 96 Mb of B. rapa BAC end sequences, total number of TRIM members of Br1, Br2, Br3, and Br4 families are roughly estimated to be present in 660 and 530 copies in B. oleracea and B. rapa genomes, respectively. Studies on insertion site polymorphisms of four elements across taxa in the tribe Brassiceae infer the taxonomic lineage and dating of the insertion time. Active roles of the TRIM elements for evolution of the duplicated genes are inferred in the highly replicated Brassica genome.

Base Sequence↗

PubMed2006

Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra.

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG(n):dC(n) and dA(n):dT(n) double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG(5)C(5) and dA(5)T(5) double helices in D(2)O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP6-31G(*) calculations for the nine basis modes. The simulated 2D IR spectra of dG(n):dC(n) double helix in D(2)O solution are directly compared with closely related experimental results. The 2D IR spectra of dG(n):dC(n) and dA(n):dT(n) are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Base Pairing↗

PubMed2006

Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa.

Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred approximately 0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.

Brassica rapa↗

PubMed2005

A basic helix-loop-helix transcription factor regulates cell elongation and seed germination.

Plants are sessile and rely on a wide variety of growth hormones to adjust growth and development in response to internal and external stimuli. We have identified a gene, designated NAN, encoding a basic helix-loop-helix (bHLH) transcription factor that regulates cell elongation and seed germination in plants. NAN has an HLH motif in its C-terminal region but does not have any other discernible homologies to bHLH proteins. A bipartite nuclear localization signal is located close to the HLH motif. An Arabidopsis mutant, nan-1D, in which NAN is activated by the insertion of the 35S enhancer, exhibits growth retardation with short hypocotyls and curled leaves. It is also characterized by reduced seed germination and apical hook formation, symptomatic of GA deficiency or disrupted GA signaling. The phenotypic effects of nan-1D were increased by treatment with paclobutrazol (PAC), an inhibitor of gibberellic acid (GA) biosynthesis. NAN is constitutively expressed throughout the life cycle. Our observations indicate that NAN has a housekeeping role in plant growth and development, particularly in seed germination and cell elongation, and that it may modulate GA signaling.

Amino Acid Sequence↗

PubMed2005

Inhibitory effect of luteolin on TNF-alpha-induced IL-8 production in human colon epithelial cells.

Interleukin (IL)-8 plays a central role in the initiation and maintenance of inflammatory responses in the inflammatory bowel disease. The proinflammatory cytokine-mediated production of IL-8 requires activation of various kinases, which leads to the IkappaB degradation and NF-kappaB activation. In this study, we investigated the role of luteolin, a major flavonoid of Lonicera japonica, on TNF-alpha-induced IL-8 production in human colonic epithelial cells. HT29 cells were stimulated with TNF-alpha in the presence or absence of luteolin. IL-8 production was measured by enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) analysis, and the mitogen-activated protein kinases (MAPKs) activation and IkappaB degradation were determined by Western blot analysis. NF-kappaB activation was assessed by the electrophoretic motility shift assay (EMSA). Luteolin suppressed TNF-alpha-induced IL-8 production in dose-dependent manner. In addition, luteolin inhibited TNF-alpha-induced phosphorylation of p38 MAPK and extracellular-regulated kinases (ERK), IkappaB degradation, and NF-kappaB activation. These results suggest that luteolin has the inhibitory effects on TNF-alpha-induced IL-8 production in the intestinal epithelial cells through blockade in the phosphorylation of MAPKs, following IkappaB degradation and NF-kappaB activation.

Anti-Inflammatory Agents↗

PubMed2005

Inhibition of interleukin-8 production in the human colonic epithelial cell line HT-29 by 18 beta-glycyrrhetinic acid.

Interleukin (IL)-8 plays a central role in the initiation and maintenance of inflammatory responses in the inflammatory bowel disease. The proinflammatory cytokine-mediated production of IL-8 requires activation of various kinases, which leads to the I kappa B degradation and NF-kappa B activation. We investigated the role of 18 beta-glycyrrhetinic acid (GA), a saponin isolated from licorice roots, on TNF-alpha-induced IL-8 production in human colonic epithelial cells. HT29 cells were stimulated with TNF-alpha in the presence or absence of GA (1, 5 or 10 microM). IL-8 production was measured by enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction analysis, and the mitogen-activated protein kinases (MAPKs) activation and I kappa B alpha degradation were determined by Western blot analysis. GA suppressed TNF-alpha-induced IL-8 production in a concentration-dependent manner. In addition, GA inhibited TNF-alpha-induced phosphorylation of p38 MAPK and extracellular-regulated kinases (ERK), I kappa B alpha degradation, and NF-kappa B activation. These results suggest that GA has the inhibitory effects on TNF-alpha-induced IL-8 production in the intestinal epithelial cells through blockade in the phosphorylation of MAPKs, following I kappa B alpha degradation and NF-kappa B activation.

Blotting, Western↗

PubMed2004

Acanthoic acid inhibits IL-8 production via MAPKs and NF-kappaB in a TNF-alpha-stimulated human intestinal epithelial cell line.

BACKGROUND: Intestinal epithelial cells (IECs) can produce cytokines and chemokines that play an important role in the mucosal immune response. Regulation of this production is important to prevent inflammatory tissue damage. The root and stem barks of Acanthopanax species have been used as a tonic and sedative as well as in the treatment of rheumatism and diabetes. The aim of this study was to examine the inhibitory effect of acanthoic acid isolated from Acanthopanax koreanum (Araliaceae), on IL-8 production via mitogen-activated protein kinases (MAPKs) and nuclear factor-kappa B (NF-kappaB) in TNF-alpha-stimulated human colon epithelial cells. METHODS: HT29 cells were stimulated with TNF-alpha in the presence or absence of acanthoic acid. IL-8 production was measured by enzyme-linked immunosorbent assay (ELISA) and reverse transcription-PCR (RT-PCR). MAPK activation and IkappaB/NF-kappaB expression were assessed by Western blot analysis. NF-kappaB activation was determined using immunofluorescence localization and electrophoretic mobility shift assay (EMSA). RESULTS: Acanthoic acid suppressed TNF-alpha-induced IL-8 production in a dose-dependent manner. Furthermore, acanthoic acid inhibited TNF-alpha-induced MAPKs (p38, JNK1/2, and ERK1/2) activation, IkappaB degradation, NF-kappaB nuclear translocation, and NF-kappaB/DNA binding activity. CONCLUSION: Acanthoic acid might inhibit TNF-alpha-mediated IL-8 production by blocking in both the MAPKs and NF-kappaB pathways in HT29 cells.

Cell Line↗

PubMed2004

Hepatocellular carcinoma,polymyositis,rhabdomyolysis,and acute renal failure.

A 55 yr-old man presented with progressive muscle weakness and oliguria for 5 days. Laboratory findings suggested rhabdomyolysis complicated with acute renal failure. A diagnosis of polymyositis was based upon the proximal muscle weakness on both upper and lower limbs, elevated muscle enzyme levels, muscle biopsy findings and the needle electromyography findings. The muscle biopsy showed extensive muscle necrosis and calcification. Investigations for underlying malignancy demonstrated hepatocellular carcinoma. The patient was managed with hemodialysis and high dose prednisolone. His renal function was fully recovered and his muscle power did improve slightly, but he died of a rupture of the hepatic tumor. In our view, this is an interesting case in that the hepatocellular carcinoma was associated with polymyositis and fulminant rhabdomyolysis-induced acute renal failure requiring hemodialysis.

Acute Kidney Injury↗

PubMed2003

The aqueous extract of Solanum melongena inhibits PAR2 agonist-induced inflammation.

BACKGROUND: Solanum melongena L. (Solanaceae) has antioxidant, analgesic, hypolipidemic and antiallergic activity. METHODS: The anti-inflammatory effects of the water extract of the S. melongena (SMWE) were investigated in PAR2-mediated mouse paw edema. Paw edema was induced by injection of trypsin or trans-cinnamoyl-LIGRLO-NH(2) (tc-NH(2)) into the hindpaw of mice. The SMWE (1, 5, 10, and 100 mg/kg) was orally administered 1 h before induction of inflammation. RESULTS: At doses of 5, 10, and 100 mg/kg, the SMWE showed significant inhibition of both paw edema and vascular permeability. The SMWE (10 mg/kg) significantly also inhibited PAR2 agonist-induced myeloperoxidase (MPO) activity and tumor necrosis factor (TNF)-alpha expression in paw tissue. CONCLUSION: These results demonstrate that the SMWE inhibits PAR2 agonist-induced mouse paw edema.

Animals↗

PubMed2003

Anti-inflammatory effect of Lonicera japonica in proteinase-activated receptor 2-mediated paw edema.

BACKGROUND: Lonicera japonica (Caprifoliaceae) has long been used for treatment of infectious diseases. In the present study, the anti-inflammatory effects of L. japonica water extract (AELJ) were investigated in proteinase-activated receptor 2 (PAR2)-mediated mouse paw edema. METHODS: Paw edema was induced by injection of trypsin or trans-cinnamoyl-LIGRLO-NH(2) (tc-NH(2)) into hindpaw of mice. AELJ (10, 50, 100, and 200 mg/kg) was orally administered 1 h before induction of inflammation. RESULTS: At doses of 50, 100 and 200 mg/kg, the AELJ showed significant inhibition of both change in paw thickness and vascular permeability. The AELJ (100 mg/kg) also significantly inhibited PAR2 agonists-induced myeloperoxidase (MPO) activity and tumor necrosis factor (TNF)-alpha expression in paw tissue. CONCLUSION: The present study demonstrated that AELJ has an anti-inflammatory action for PAR2-mediated paw edema.

Administration, Oral↗

PubMed2003

Expression of protease-activated receptor 2 in ulcerative colitis.

Although tryptase released from mast cells might play a key role in the pathogenesis of ulcerative colitis (UC), the role of protease-activated receptor 2 (PAR2), tryptase receptor, remains unclear in the pathogenesis of this disease. The expressions of PAR2 and tumor necrosis factor (TNF) alpha in nine UC tissues and nine normal tissues were examined by immunohistochemistry. TNF-alpha levels secreted from human leukemic mast cell line (HMC-1) after the treatment of PAR2 agonists were also measured by enzyme-linked immunosorbent assay. The PAR2 and TNF-alpha proteins were more significantly detectable in UC tissues than in normal tissues. Furthermore, 65.2% of PAR2+ cells and 66.4% of TNF-alpha+ cells in UC tissues were tryptase-positive cells. In other words, 60.6% and 46.3% of tryptase-positive cells in UC tissues were PAR2+ cells and TNF-alpha+ cells, respectively. A chi2 analysis showed correlation (p < 0.007) between PAR2 and TNF-alpha in tryptase-positive mast cells. Moreover, PAR2 agonists significantly induced the TNF-alpha secretion from HMC-1. These results indicate that the activation of the mast cells through PAR2 may be involved in the pathogenesis of UC.

Colitis, Ulcerative↗