• Asian-Australasian Journal of Animal Sciences
• /
• v.23 no.7
• /
• pp.833-847
• /
• 2010

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.

• KIPS Transactions on Computer and Communication Systems
• /
• v.3 no.1
• /
• pp.1-6
• /
• 2014

Most of the previous algorithms focus on computing the convex hull for a set of points. In this paper, we present a method for approximating the convex hull for a set of spheres with various radii in discrete space. Computing the convex hull for a set of spheres is a base technology for many applications that study structural properties of molecules. We present a voxel map data structures, where the molecule is represented as a set of spheres, and corresponding algorithms. Based on CUDA programming for using the parallel architecture of GPU, our algorithm takes less than 40ms for computing the convex hull of 6,400 spheres in average.

• Journal of The Korean Astronomical Society
• /
• v.39 no.1
• /
• pp.9-17
• /
• 2006

In an attempt to investigate star formation activity and statistical properties of clumps of high Galactic latitude clouds (HLCs), we mapped the Polaris Flare region, PF121.3+25.5, in $^{12}CO\;and\;^{13}CO$ J = 1 - 0 using SRAO 6-m telescope and also observed its 12 $^{13}CO$ peak positions in CS J = 2 - 1 with TRAO 14-m telescope. $^{13}CO$ integrated intensity map shows clearly its clumpy structure and the locations of clumps well agree with $^{12}CO$morphology. CS line is not detected toward the 12 $^{13}CO$ peak positions, so we can conclude there are no dense $(\sim10^4\;cm^{-3})$ in this region. We decomposed 105 clumps from $^{13}CO$ map using GAUSSCLUMPS algorithm. The mass of clumps ranges from $7.8\;M_{\odot}\;to\;7.4{\times}10^{-2}\;M_{\odot}$ with a total mass of $66.4\;M_{\odot}$ The mass spectrum follows a power law, dN/dM ${\propto}\;M^{-\alpha}$ with a power index of ${\alpha}=1.91{\pm}0.13$. The virial masses of clumps are in the range of $10{\sim}100M_{LTE}$ and so these clumps are considered to be gravitationally unbound.

• Molecules and Cells
• /
• v.42 no.10
• /
• pp.729-738
• /
• 2019

Autophagy is an important process for protein recycling. Oligomerization of p62/SQSTM1 is an essential step in this process and is achieved in two steps. Phox and Bem1p (PB1) domains can oligomerize through both basic and acidic surfaces in each molecule. The ZZ-type zinc finger (ZZ) domain binds to target proteins and promotes higher-oligomerization of p62. This mechanism is an important step in routing target proteins to the autophagosome. Here, we determined the crystal structure of the PB1 homo-dimer and modeled the p62 PB1 oligomers. These oligomer models were represented by a cylindrical helix and were compared with the previously determined electron microscopic map of a PB1 oligomer. To accurately compare, we mathematically calculated the lead length and radius of the helical oligomers. Our PB1 oligomer model fits the electron microscopy map and is both bendable and stretchable as a flexible helical filament.

• BMB Reports
• /
• v.57 no.5
• /
• pp.238-243
• /
• 2024

Bone marrow-derived mesenchymal stem cells (BM-MSCs) can differentiate into endothelial cells in an inflammatory microenvironment. However, the regulatory mechanisms underlying this process are not entirely understood. Here, we found that TIE2 in BM-MSCs was upregulated at the transcriptional level after stimulation with tumor necrosis factor-alpha (TNFα), a major pro-inflammatory cytokine. Additionally, the STAT-binding sequence within the proximal region of TIE2 was necessary for TNFα-induced TIE2 promoter activation. TIE2 and STAT3 knockdown reduced TNFα-induced endothelial tube formation in BM-MSCs. Among the major TNFα-activated MAP kinases (ERK1/2, JNK1/2, and p38 MAPK) in BM-MSCs, only inhibition of the p38 kinase abrogated TNFα-induced TIE2 upregulation by inhibiting the JAK-STAT signaling pathway. These findings suggest that p38 MAP contributes to the endothelial differentiation of BM-MSCs by activating the JAK-STAT-TIE2 signaling axis in the inflammatory microenvironment.

• Biomolecules & Therapeutics
• /
• v.25 no.6
• /
• pp.641-647
• /
• 2017

Galangin (3,5,7-trihydroxyflavone) is a polyphenolic compound abundant in honey and medicinal herbs, such as Alpinia officinarum. In this study, we investigated the anti-inflammatory effects of galangin under in vitro and in vivo neuroinflammatory conditions caused by polyinosinic-polycytidylic acid (poly(I:C)), a viral mimic dsRNA analog. Galangin suppressed the production of nitric oxide, reactive oxygen species, and pro-inflammatory cytokines in poly(I:C)-stimulated BV2 microglia. On the other hand, galangin enhanced anti-inflammatory interleukin (IL)-10 production. Galangin also suppressed the expression of pro-inflammatory markers in poly(I:C)-injected mouse brains. Further mechanistic studies showed that galangin inhibited poly(I:C)-induced nuclear factor (NF)-${\kappa}B$ activity and phosphorylation of Akt without affecting MAP kinases. Interestingly, galangin increased the expression and transcriptional activity of peroxisome proliferator-activated receptor (PPAR)-${\gamma}$, known to play an anti-inflammatory role. To investigate whether PPAR-${\gamma}$ is involved in the anti-inflammatory function of galangin, BV2 cells were pre-treated with PPAR-${\gamma}$ antagonist before treatment of galangin. We found that PPAR-${\gamma}$ antagonist significantly blocked galangin-mediated upregulation of IL-10 and attenuated the inhibition of tumor necrosis factor (TNF)-${\alpha}$ and IL-6 in poly(I:C)-stimulated microglia. In conclusion, our data suggest that PI3K/Akt, NF-${\kappa}B$, and PPAR-${\gamma}$ play a pivotal role in mediating the anti-inflammatory effects of galangin in poly(I:C)-stimulated microglia.

• Horticultural Science & Technology
• /
• v.32 no.6
• /
• pp.745-752
• /
• 2014

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is an economically important vegetable crop as a source of the traditional food Kimchi in Korea. Although many varieties exhibiting desirable traits have been developed by the conventional selective breeding approach, breeding related to abiotic or biotic stresses, such as a particular pests or diseases, or tolerance to climatic conditions, is likely to be slow. This could be helped by an efficient method for selection from various, rapidly-evolved genetic resources on the basis of molecular markers. In particular, the Brassica genome sequencing project enables genome-wide discovery of genes or genetic variants associated with agricultural traits. We here discuss the recent progress in the field of Chinese cabbage breeding with regard to the application of molecular markers.

• Mycobiology
• /
• v.45 no.4
• /
• pp.362-369
• /
• 2017

We assessed the regulation of cryparin, a class II hydrophobin, using three representative mitogen-activated protein kinase (MAPK) pathways in Cryphonectria parasitica. Mutation of the CpSlt2 gene, an ortholog of yeast SLT2 in the cell wall integrity (CWI) pathway, resulted in a dramatic decrease in cryparin production. Similarly, a mutant of the CpBck1 gene, a MAP kinase kinase kinase gene in the CWI pathway, showed decreased cryparin production. Additionally, mutation of the cpmk1 gene, an ortholog of yeast HOG1, showed decreased cryparin production. However, mutation of the cpmk2 gene, an ortholog of yeast Kss1/Fus3, showed increased cryparin production. The easy-wet phenotype and accumulation of the cryparin transcript in corresponding mutants were consistent with the cryparin production results. In silico analysis of the promoter region of the cryparin gene revealed the presence of binding motifs related to downstream transcription factors of CWI, HOG1, and pheromone responsive pathways including MADS-box- and Ste12-binding domains. Real-time reverse transcriptase PCR analyses indicated that both CpRlm1, an ortholog of yeast RLM1 in the CWI pathway, and cpst12, an ortholog of yeast STE12 in the mating pathway, showed significantly reduced transcription levels in the mutant strains showing lower cryparin production in C. prasitica. However, the transcription of CpMcm1, an ortholog of yeast MCM1, did not correlate with that of the mutant strains showing downregulation of cryparin. These results indicate that three representative MAPK pathways played a role in regulating cryparin production. However, regulation varied depending on the MAPK pathways: the CWI and HOG1 pathways were stimulatory, whereas the pheromone-responsive MAPK was repressive.

• The Bulletin of The Korean Astronomical Society
• /
• v.44 no.1
• /
• pp.42.2-42.2
• /
• 2019

Turbulence is one of the natural phenomena in molecular clouds. It affects gas density and velocity fluctuation within the molecular clouds and controls the mode and tempo of star formation. However, despite many years of study, the properties of turbulence remain poorly understood. As part of the Taeduk Radio Astronomy Observatory (TRAO) Key Science Program (KSP), "mapping Turbulent properties In star-forming MolEcular clouds down to the Sonic scale (TIMES; PI: Jeong-Eun Lee)", we have fully mapped two star-forming molecular clouds, the Orion A and the Ophiuchus molecular clouds, in 3 sets of lines ($^{13}CO$ J=1-0, $C^{18}O$ J=1-0, HCN J=1-0, $HCO^+$ J=1-0, CS J=2-1, and $N_2H^+$ J=1-0) using the TRAO 14-m telescope. We apply a statistical analysis, Principal Component Analysis (PCA), which can recover an underlying turbulent-power spectrum from an observed P-P-V spectral map. We compare turbulence properties not only between the two clouds, but also between different parts within each cloud. We present the first result of our observation program.

• Molecules and Cells
• /
• v.42 no.10
• /
• pp.702-710
• /
• 2019

Neuroinflammation is an important contributor to the pathogenesis of neurodegenerative disorders including Parkinson's disease (PD). We previously reported that our novel synthetic compound KMS99220 has a good pharmacokinetic profile, enters the brain, exerts neuroprotective effect, and inhibits $NF{\kappa}B$ activation. To further assess the utility of KMS99220 as a potential therapeutic agent for PD, we tested whether KMS99220 exerts an anti-inflammatory effect in vivo and examined the molecular mechanism mediating this phenomenon. In 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated mice, oral administration of KMS99220 attenuated microglial activation and decreased the levels of inducible nitric oxide synthase and interleukin 1 beta ($IL-1{\beta}$) in the nigrostriatal system. In lipopolysaccharide (LPS)-challenged BV-2 microglial cells, KMS99220 suppressed the production and expression of $IL-1{\beta}$. In the activated microglia, KMS99220 reduced the phosphorylation of $I{\kappa}B$ kinase, c-Jun N-terminal kinase, and p38 MAP kinase; this effect was mediated by heme oxygenase-1 (HO-1), as both gene silencing and pharmacological inhibition of HO-1 abolished the effect of KMS99220. KMS99220 induced nuclear translocation of the transcription factor Nrf2 and expression of the Nrf2 target genes including HO-1. Together with our earlier findings, our current results show that KMS99220 may be a potential therapeutic agent for neuroinflammation-related neurodegenerative diseases such as PD.