• Journal of Life Science
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• v.19 no.7
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• pp.905-916
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• 2009

Pinelliae rhizoma (Pr, 半夏) is a traditional medicine used in the treatment of incipient stroke. We investigated the effects of Pr on gene expression in a hypoxic model using cultured rat cortical cells. Pr (2.5 $\mu$g/ml) was added to the culture medium on DIV 12. A hypoxic shock (2% 0$_2$/5% CO$_2$, 37$^{\circ}$C, 3 hr) was given two days later (on DIV 14), and total mRNAs were isolated at 24 hr post-shock from both Pr-treated samples and untreated control cultures. Microarray using TwinChip $^{TM}$ Rat-5K (Digital Genomics, Seoul) indicated that Pr upregulated genes for cell growth and differentiation (tubb5, tgfa, ptpn11, n-ras, pdgfa) and antiapoptosis (mcl-1), while downregulating the apoptosis-induced gene (tieg). Therefore, it is interpreted that Pr protects neurons from hypxoic shock by maintaining cell growth and differentiation and by preventing apoptosis.

• Molecules and Cells
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• v.39 no.4
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• pp.352-357
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• 2016

Vertebrate neurogenesis requires inhibition of endogenous bone morphogenetic protein (BMP) signals in the ectoderm. Blocking of BMPs in animal cap explants causes the formation of anterior neural tissues as a default fate. To identify genes involved in the anterior neural specification, we analyzed gene expression profiles using a Xenopus Affymetrix Gene Chip after BMP-4 inhibition in animal cap explants. We found that the xCyp26c gene, encoding a retinoic acid (RA) degradation enzyme, was upregulated following inhibition of BMP signaling in early neuroectodermal cells. Whole-mount in situ hybridization analysis showed that xCyp26c expression started in the anterior region during the early neurula stage. Overexpression of xCyp26c weakly induced neural genes in animal cap explants. xCyp26c abolished the expression of all trans-/cis-RA-induced posterior genes, but not basic FGF-induced posterior genes. Depletion of xCyp26c by morpholino-oligonucleotides suppressed the normal formation of the axis and head, indicating that xCyp26c plays a critical role in the specification of anterior neural tissue in whole embryos. In animal cap explants, however, xCyp26c morpholinos did not alter anterior-to-posterior neural tissue formation. Together, these results suggest that xCyp26c plays a specific role in anterior-posterior (A-P) neural patterning of Xenopus embryos.

• Biomolecules & Therapeutics
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• v.25 no.2
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• pp.112-121
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• 2017

Drug-induced liver injury (DILI) is the serious and fatal drug-associated adverse effect, but its incidence is very low and individual variation in severity is substantial. Acetaminophen (APAP)-induced liver injury accounts for >50% of reported DILI cases but little is known for the cause of individual variations in the severity. Intrinsic genetic variation is considered a key element but the identity of the genes was not well-established. Here, pre-biopsy method and microarray technique was applied to uncover the key genes for APAP-induced liver injury in mice, and a cause and effect experiment employing quantitative real-time PCR was conducted to confirm the correlation between the uncovered genes and APAP-induced hepatotoxicity. We identified the innately and differentially expressed genes of mice susceptible to APAP-induced hepatotoxicity in the pre-biopsied liver tissue before APAP treatment through microarray analysis of the global gene expression profiles (Affymetrix $GeneChip^{(R)}$ Mouse Gene 1.0 ST for 28,853 genes). Expression of 16 genes including Gdap10, Lpl, Gabra3 and Ccrn4l were significantly different (t-test: FDR <10%) more than 1.5 fold in the susceptible animals than resistant. To confirm the association with the susceptibility to APAP-induced hepatotoxicity, another set of animals were measured for the expression level of selected 4 genes (higher two and lower two genes) in the liver pre-biopsy and their sensitivity to APAP-induced hepatotoxicity was evaluated by post hoc. Notably, the expressions of Gabra3 and Lpl were significantly correlated with the severity of liver injury (p<0.05) demonstrating that these genes may be linked to the susceptibility to APAP-induced hepatotoxicity.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.102-111
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• 2016

The goal of this study was to characterize the BrDSR (Drought Stress Resistance in B. rapa) gene and to identify the expression network of drought-inducible genes in Chinese cabbage under drought stress. Agrobacterium-mediated transformation was conducted using a B. rapa inbred line ('CT001') and the pSL100 vector containing the BrDSR full length CDS (438 bp open reading frame). Four transgenic plants were selected by PCR and the expression level of BrDSR was approximately 1.9-3.4-fold greater than that in the wild-type control under drought stress. Phenotypic characteristics showed that BrDSR over-expressing plants were resistant to drought stress and showed normal growth habit. To construct a co-expression network of drought-responsive genes, B. rapa 135K cDNA microarray data was analyzed to identify genes associated with BrDSR. BrDSR was directly linked to DARK INDUCIBLE 2 (DIN2, AT3G60140) and AUTOPHAGY 8H (ATG8H, AT3G06420) previously reported to be leaf senescence and autophagy-related genes in plants. Taken together, the results of this study indicated that BrDSR plays a significant role in enhancement of tolerance to drought conditions.

• Nutrition Research and Practice
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• v.2 no.4
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• pp.289-294
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• 2008

Pre-B-cell leukemia transcription factor 1 (PBX1), which is located on chromosome 1q23, was recently reported to be associated with type 2 diabetes mellitus. We examined whether single nucleotide polymorphisms (SNPs) of the PBX1 gene are associated with overweight/obesity in a Korean population. We genotyped 66 SNPs in the PBX1 gene and investigated their association with clinical phenotypes found in 214 overweight/obese subjects and 160 control subjects using the Affymetrix Targeted Genotyping chip array. Seven SNPs (g.+75l86C>T, g.+78350C>A, g.+80646C>T, g.+138004C>T, g.+185219G>A, g.+191272A>C, and g.+265317T>A) were associated with the risk of obesity in three models (codominant, dominant, and recessive) (P=0.007-0.05). Haplotype 1 (CAC) and 3 (TAC) of block 3 and haplotype 2 (GGAAT) of block 10 were also strongly associated with the risk of obesity. In the control group, subjects that had homozygote for the major allele for both g.+185219G>A and g.+191272A>C showed lower high density lipoprotein-cholesterol (HDL-C) level compared to those possessing the minor allele, suggesting that the association between the homozygote for the major allele for both g.+185219G>A and g.+191272A>C and HDL-C is attributable to the increased risk of obesity. This study suggests that the PBX1 gene is a possible risk factor in overweight/obese patients.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.269-269
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• 2022

Pre-harvest sprouting (PHS) on rice panicles is getting problematic in recent several years in Korea due to climate changes such as high temperature and more frequent typhoons during harvesting season. PHS negatively affects grain quality severely and also yield. Genetic improvement of Korean varieties (Oryza sativa ssp. japonica) through a marker assisted-backcross breeding (MAB) with the known PHS resistant genes must be one of ideal solutions. However, the final breeding products of MAB occasionally exhibit unwanted traits, especially the cross between genetically distant parents. This might be caused by linkage drag and/or presence of the gene-unlinked donor introgressions, resulting that the final products could not be released to the farmers. The major PHS resistance gene, Sdr4 (Seed dormancy 4) originated from an indica cultivar, Kasalath was selected as a donor gene. In order to avoid unexpected phenotypes in the breeding products, we performed a precision marker-based breeding (PMBB) consisting of foreground, recombinant, and background selections (FS, RS, and BS) which aim to develop 'single small introgression lines' (~100 kb introgression). Korean varieties (Ilpum and Gopum) were crossed with Kasalath. We developed Sdr4-allele specific markers for FS and a set of polymorphic flanking markers near the Sdr4 (-350kb and +420kb) for RS. To minimize linkage drag, the small introgression (< 125kb) containing Sdr4 was selected in Ilpum background (BC₂F₄) through 1^st RS with ~1,200 F₂ or BC₁F₂ plants (one side trimmed) and then 2^nd RS with ~1,000 progenies from the 1^st RS selected plants (another side trimmed). After RS, the selected lines were genotyped by using Infinium 7K SNP chip to detect other donor introgressions and the lines were backcrossed. Currently BS is on-going from the backcross-derived progenies with BS markers to remove residual introgressions. During the PMBB process, genetic effect of Sdr-4-Kasalath allele was confirmed in Ilpum and Gopum backgrounds by PHS phenotyping using the segregating BC₂F₃ or BC₁F₄ materials. The Sdr4 PMBB lines in Ilpum background (< 125kb introgression) will be valuable genetic resources to improve PHS resistance in modem popular temperate japonica varieties.

• Tuberculosis and Respiratory Diseases
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• v.65 no.6
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• pp.495-503
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• 2008

Background: Epigenetic alterations in certain genes are now known as at least important as genetic mutation in pathogenesis of cancer. Especially abnormal hypermethylation in or near promoter region of tumor suppressor genes (TSGs) are known to result in gene silencing and loss of gene function eventually. The authors tried to search for new lung cancer-specific TSGs which have CpG islands and HpaII sites, and are thought to be involved in carcinogenesis by epigenetic mechanism. Methods: Tumor tissue and corresponding adjacent normal tissue were obtained from 10 patients who diagnosed with non small cell lung cancer (NSCLC) and underwent surgery in Konyang university hospital in 2005. Methylation profiles of promoter region of 21 genes in tumor tissue & non-tumor tissue were examined with HpaII-MspI methylation microarray (Methyl-Scan DNA chip$^{(R)}$, Genomic tree, Inc, South Korea). The rates of hypermethylation were compared in tumor and non-tumor group, and as a normal control, we obtained lung tissue from two young patients with pneumothorax during bullectomies, methylation profiles were examined in the same way. Results: Among the 21 genes, 10 genes were commonly methylated in tumor, non-tumor, and control group. The 6 genes of APC, AR, RAR-b, HTR1B, EPHA3, and CFTR, among the rest of 11 genes were not methylated in control, and more frequently hypermethylated in tumor tissue than non-tumor tissue. Conclusion: In the present study, HTR1B, EPHA3, and CFTR are suggested as possible novel TSGs of NSCLC by epigenetic mechanism.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.347-358
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• 2016

Brassinosteroid (BR), a plant steroid hormone, plays key roles in numerous growth and developmental processes as well as tolerance to both abiotic and biotic stress. To understand the biological networks involved in BR-mediated signaling pathways and stress tolerance, we performed comparative genome-wide transcriptome analysis of a constitutively activated BR bes1-D mutant with an Agilent Arabidopsis $4{\times}44K$ oligo chip. As a result, we newly identified 1,091 (562 up-regulated and 529 down-regulated) significant differentially expressed genes (DEGs). The combination of GO enrichment and protein network analysis revealed that stress-related processes, such as metabolism, development, abiotic/biotic stress, immunity, and defense, were critically linked to BR signaling pathways. Among the identified gene sets, we confirmed more than a 6-fold up-regulation of NB-ARC and FLS2 in bes1-D plants. However, some genes, including TIR1, TSA1 and OCP3, were down-regulated. Consistently, BR-activated plants showed higher tolerance to drought stress and pathogen infection compared to wild-type controls. In this study, we newly developed a useful, comprehensive method for large-scale identification of critical network and gene sets with global transcriptome analysis using a microarray. This study also showed that gain of function in the bes1-D gene can regulate the adaptive response of plants to various stressful conditions.

• Journal of Life Science
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• v.23 no.1
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• pp.116-124
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• 2013

The aim was to examine resistance exercise-related genes after 8 weeks of resistance training. Thirty-two male Sprague-Dawley rats were divided into four groups: 4 weeks sedentary (4 wks CON, n=8), 8 weeks sedentary (8 wks CON, n=8), 4 weeks exercise training (4 wks REG, n=8), and 8 weeks exercise training (8 wks REG, n=8). The rats were trained to climb a 1-m vertical incline (85-degree), with weights secured to their tails. They climbed 10 times, 3 days per week, for 8 consecutive weeks. Skeletal muscle was taken from the flexor halucis longus after the exercise training. After separating the total RNA, large-scale gene expression was investigated by beadarray (Illumina RatRef-12 Expression BeadChip) analysis, and qPCR was used to inspect the beadarray data and to analyze the RNA quantitatively. The detection p-value for the genes was p<0.01, the M-value {M=$log_2$(condition)-$log_2$(reference)} was >1.0, and the DiffScore was >20. In total, the expression of 30 genes significantly increased 4 weeks after the exercise training, and the expression of six genes decreased. At 8 weeks, the expression of five genes significantly increased and that of 12 decreased. Several genes are potentially involved in resistance exercise and muscle hypertrophy, including 1) regulation of cell growth (IGFBP1, PLA2G2A, OKL38); 2) myogenesis (CSRP3); 3) tissue regeneration and muscle development (MUSTN1, MYBPH); 4) hypertrophy (CYR61, ATF3, NR4A3); and 5) glucose metabolism (G6PC, PCK1). These results may help to explain previously reported physiological changes of the skeletal muscle and suggest new avenues for further investigation.

• Clinical and Experimental Pediatrics
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• v.48 no.2
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• pp.197-203
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• 2005

Purpose : Changes in metalloproteinases(MMP) activity have been demonstrated in several disease states, including rheumatoid arthritis and tumor metastasis. More importantly, increased myocardial MMP activity has been reported to occur in both clinical and experimental forms of dilated cardiomyopathy. There was no report about MMP in adriamycin(ADR)-induced cardiomyopathy. The purpose of this study was to investigate gene expression of MMP and tissue inhibitor of metalloproteinases(TIMP) in ADR-induced cardiomyopathy and clarify the relationship between MMP and cytokines. Methods : Male Sprague-Dawley rats were divided into two groups. The first group was control. The second group was given intraperitoneal injections of ADR(5 mg/kg) twice a week over two weeks. Serum concentrations of MMP, TIMP, interleukin(IL)-6 and tumor necrosis factor(TNF)-${\alpha}$ were measured. RNA extraction was performed from frozen rat hearts. Reverse transcription polymerase chain reaction(RT-PCR) was employed. cDNA Microarray analysis was performed by using a set of 5,184 sequence-verified rat cDNA clones. Results : Serum MMP and TIMP levels were not significantly different between the two groups. IL-6 was $36.8{\pm}2.8pg/mL$ and TNF-${\alpha}$ $2.2{\pm}2.7pg/mL$ in the ADR group. They were significantly higher than in the control group. Serum MMP correlated significantly with TNF-${\alpha}$(r=0.41, P<0.05). There was no gene expression of MMP, IL-6 or TNF-${\alpha}$ in the hearts of both groups. Gene expression of TIMP was significantly depressed in the hearts of the ADR group. Conclusion : These results suggested a potential role for TNF-${\alpha}$ in the regulation of extracellular matrix remodeling in ADR induced cardiomyopathy. Rapid screening of multiple decreased gene expression by DNA chip may be a useful diagnostic test to detect early cardiac injury before developing ADR induced cardiomyopathy.