• KOREAN JOURNAL OF CROP SCIENCE
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• v.53 no.1
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• pp.85-92
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• 2008

An RIL population from a Shinpaldalkong2/GC83006 cross was employed to identify quantitative trait loci (QTL) associated with agronomic traits in soybean. The genetic map consisted of 127 loci which covered about 3,000cM and were assigned into 20 linkage groups. Phenotypic data were collected for the following traits; plant height, leaf area, flowering time, pubescence color, seed coat color and hilum color in 2005. Seed weight was evaluated using seeds collected in 2003 to 2005 at Suwon and in 2005 at Pyeongchang and Miryang sites. Three QTLs were associated with 100-seed weight in the combined analysis across three years. Among the three QTLs related to seed weight, all GC83006 alleles on LG O ($R^2\;=\;12.5$), LG A1 ($R^2\;=\;10.1$) and LG C2 ($R^2\;=\;11.5$) increased the seed weight. A QTL conditioning plant height was linked to markers including Satt134 (LG C2, $R^2\;=\;25.4$), and the GC83006 allele increased plant height at this QTL locus. For two QTLs related to leaf area, 1aM on LG M ($R^2\;=\;10.0$) and laL on LG L ($R^2\;=\;8.6$), the Shinpaldalkong2 alleles had positive effect to increase the leaf area. Satt134 on LG C2 ($R^2\;=\;41.0$) was associated with QTL for days to flowering. Satt134 (LG C2) showed a linkage to a gene for pubescence color. Satt363 (LG C2) and Satt354 (LG I) were linked to the hilum color gene, and Sat077 (LG D1a) was linked to the seed coat color. The QTL conditioning plant height was in the similar genomic location as the QTLs for days to flowering in this population, indicating pleiotropic effect of one gene or the tight linkage of several genes. These linked markers would be useful in marker assisted selection for these traits in a soybean breeding program.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.559-568
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• 2007

Recently, copy number variations (CNV) of genes or genomic segments have been intensively studied and various analysis methods have been developed. In this study, quantitative oligonucleotide ligation assay (qOLA) was applied to investigate CNV of KIT gene in the Landrace breed. A combined assay using qOLA and pyrosequencing, 6 genotype classes, I1/I1 or I3/i (IBe), I1/I2 or I3/IP, I1/I3, I1/IP or I2/i (IBe), I2/I2and I2/IP, were identified from 44 Landrace pigs. Genotype assignment using grouping features of measurements on a scatter plot showed 100% agreement with those using a statistical assignment by PROC FASTCLUS procedure implemented in the SAS package. Two versions (3100 and 3130) of ABI sequencers gave the same genotyping results, indicating there was no influence on qOLA by different versions of instrument, however, the means of standard deviation and coefficient of variation from the qOLA on a ABI 3130 (2.33 and 4.10) was lower than those from the qOLA on a ABI 3100 (2.67 and 4.81). Effect of proteinase K treatment on the PCR product followed by qOLA was very clear because noise peaks were disappeared and the observed ration fit better to the reference ratio corresponding to each genotype.

• Journal of Embryo Transfer
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• v.31 no.3
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• pp.227-233
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• 2016

This study was conducted to analyze the effect of single nucleotide polymorphisms (SNPs) on the equine chromosomes (ECA) 3 for the body conformations of 12 month of age in Jeju crossbred (Jeju horses ${\times}$ Thoroughbred). A total of 199 Jeju crossbred horse samples were obtained from the National Institute of Subtropical Livestock Research Institute for this study. To correctly estimate the body conformations, we measured thirteen elements relevant to the body conformation such as body weight, wither height, body length for all the 199 horses at 12 month of age. Furthermore, all the horses were genotyped using four SNPs including the BIEC2-808466, BIEC2-808543, BIEC2-808967, BIEC2-809370, of which genomic coordinates range approximately from 105.1Mbp to 110 Mbp in the ECA3. For the phenotypic data sets, the average body weight was $193.7{\pm}24.5kg$ and the height was $124.5{\pm}4.0cm$. As for the genotypic data, the miner allele frequencies of the SNPs were shown to be varied from 0.01 to 0.291. Using the phenotypic and genotypic data sets, analysis of covariance was performed to find any association between those SNP genotypes and body conformations, using year of birth, month of birth, sex, and parity as the covariance components. The result showed that alternative genotypes in the BIEC2-808967 and BIEC2-809370 SNPs were significantly associated with the body length (P<0.05) and the wither height (P<0.05) respectively in the Jeju crossbred horses. Therefore, it is estimated that there are significant associations in the body conformation of 12 month of age of Jeju crossbred for those two SNPs used in this study.

• Clinical and Experimental Pediatrics
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• v.45 no.7
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• pp.884-890
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• 2002

Purpose : Henoch-Schonlein purpura(HSP) nephritis has been reported to vary from 25 to 50% among HSP patients and is a common cause of chronic glomerulonephritis in children. In our study, we evaluated the distribution and the association of the Insertion/Deletion(I/D) polymorphism of angiotensin converting enzyme(ACE) gene with clinical manifestations, particularly proteinuria in children with HSP nephritis, compared with that in HSP. Methods : ACE gene polymorphism was determined in children with HSP nephritis(n=33) and HSP(n=28) who were diagnosed in Busan Paik hospital from January 1996 to June 2001. The I/D polymorphism of ACE gene was determined by PCR amplication of genomic DNA. Results : The ACE I/D genotype frequency was DD : 25%, ID : 50%, II : 25% in HSP and DD : 24 %, ID : 46%, II : 30% in HSP nephritis, there was no significant difference in the genotype and allele frequencies between two groups. When statistical analysis was done according to the presence of D allele, the amount of 24-hour urinary protein excretion and the incidence of moderate to heavy proteinuria(>$500mg/m^2/day$) at onset and last follow-up were higher in DD/ID genotype than in those in II genotype, but these differences were not statistically significant. Conclusion : We suggest a lack of association between I/D polymorphism of ACE gene and clinical manifestations in children with HSP nephritis. However, further follow-up studies based on a sufficient number of patients and long term follow up periods are necessary to confirm the role of I/D polymorphism of ACE gene in children with HSP nephritis.

• Tuberculosis and Respiratory Diseases
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• v.61 no.4
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• pp.374-383
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• 2006

Background: Ethyl pyruvate (EP) is a derivative of pyruvate that has recently been identified by both various in vitro and in vivo studies to have antioxidant and anti-inflammatory effects. The aim of this study was to determine the effect of EP on lipopolysaccharide (LPS)-induced acute lung injury (ALI). Methods: 5 weeks old, male BALB/c mice were used. ALI was induced by an intratracheal instillation of LPS 0.5mg/Kg/$50{\mu}L$ of saline. The mice were divided into the control, LPS, EP+LPS, and LPS+EP groups. In the control group, balanced salt solution was injected intraperitoneally 30 minutes before or 9 hours after the intratracheal instillation of saline. In the LPS group, a balanced salt solution was also injected intraperitoneally 30 minutes before or 9 hours after instillation the LPS. In the EP+LPS group, 40mg/Kg of EP was injected 30 minutes before LPS instillation. In the LPS+EP group, 40mg/Kg of EP was injected 9 hours after LPS instillation. The TNF-$\alpha$ and IL-6 concentrations in the bronchoalveolar lavage fluid (BALF), and that of NF-$\kappa$B in the lung tissue were measured in the control, LPS and EP+LPS groups at 6 hours after instillation of saline or LPS, and the ALI score and myeloperoxidase (MPO) activity were measured in all four groups 24 and 48 hours after LPS instillation, respectively. Results: The TNF-$\alpha$ and IL-6 concentrations were significantly lower in the EP+LPS group than in the LPS group (p<0.05). The changes in the concentration of these inflammatory cytokines were strongly correlated with that of NF-$\kappa$B (p<0.01). The ALI scores were significantly lower in the EP+LPS and LPS+EP groups compared with the LPS group (p<0.05). In the EP+LPS group, the MPO activity was significantly lower than the LPS group (p=0.019). Conclusion: EP, either administered before or after LPS instillation, has protective effects against the pathogenesis of LPS-induced ALI. EP has potential theurapeutic effects on LPS-induced ALI.

• THE JOURNAL OF KOREAN ORIENTAL ONCOLOGY
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• v.6 no.1
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• pp.81-97
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• 2000

Objectives: This experimental study was carried out to evaluate the effects of aqueous and methanol extracts of Hedyotis diffusa which has long been used for cancer treatment in oriental medicines on the induction of apoptotic cell death in human lymphoid leukemia cell line, HL-60. Methods: Cells were treated with various concentrations (200 to $0.4{\mu}g$) and periods (6 to 30 hr) of $H_2O$ and methanol extracts of Hedyotis diffusa. Then, cells were tested for viability by MTT assay. Cells wrere treated with $200{\mu}g/ml$ of methanol extract fork various periods. Genomic DNA was isolated, separated, on 1.5% agarose gels, stained with ethidium bromide and visualized under UV light. Cells were treated with $200{\mu}g/ml$ of each extract for 16 hr. Then, cells were treated with Hoechst dye 33342 and observed by fluorescence microscopy. Cells were treated with various doses of each for 12 hr and $100{\mu}g/ml$ of methanol extract for various periods. Lysate from the cells used to measure the activity of Caspase-1 and-3 proteases by using fluorogenic peptide substrates including acetyl-YVAD-AMC and acetyl-DEVD-AMC, respectively. Cells were treated with $200{\mu}g/ml$ of each extract for various periods. Cell lysates were immunoprecipated with anti-JNKl antibodies. The immune complex was reacted with $32^p-ATP$ and c-Jun as a substrate. The phosphotransferase activity of JNKI was measured by using PhosphoImage analyzer (Fuji Co., Japan). Nuclear extracts were isolated and incubated with oligonucleotide probe of $NF-{\kappa}B$. Transcriptional activation of ${\kappa}B$ was measured by using EMSA and visualized by PhosphoImage analyzer (Fuji Co, Japan). Cell lysates were prepared and analyzed by Western blotting with anti-Bc12 antibodies and anti-Bax antibodies. Cells were pretreated with various doses of methanol extract for 2 hr. Then, the extract was removed by centrifugation. Cells were resuspended with RPMI-1640 media containing 0.3% agarose, 10% FBS, overlayred onto bottom layer agarose and incubated at $CO_2$ incubator for 6 days. The number of colony was counted under light microscopy ($\time100$). Results: The death of HL-60 cells was markedly induced by the addition of methanol extract of Hedyotis diffusa in a dose and time-dependent manners. The apoptotic characteristic ladder pattern of DNA strand break was observed in death of HL-60 cells. In addition, it was shown nucleus chromatin condensation and fragmentation under Hoechst staining. Therefore, Hedyotis diffusa extract-induced death of HL-60 cells is mediated by apoptotic signaling processes. The activity of Caspase 3-like proteases remained in a basal level in HL-60 cells treated with aqueous extract of Hedyotis diffusa. However, it was markedly increased in HL-60 cells treated with methanol extract of Hedyotis diffusa. In addition, the phosphotransferase activity of JNKl was increased in HL-60 cells treated with methanol extract of Hedyotis diffusa. Furthermore, the activation of transcriptional activator, $NF-{\kappa}B$ was markedly induced by methanol extract of Hedyotis diffusa. Anti-apoptotic Bc12 was cleaved into 23Kda fragment by treatment of methanol extract of Hedyotis diffusa. However, expression of proapoptotic Bax protein was increased by treatment of methanol extract of Hedyotis diffusa in a time-dependent manner. Furthermore, methanol extract markedly inhibited the colony forming efficiency of HL-60 cells in semisolid agar culture. Conclusions: Above results suggest that methanol extract of Hedyotis diffusa induces the apoptotic death of human leukemic HL-60 cells via activations of Caspase-3 proteases, JNKI, transcriptional activator $NF-{\kappa}B$, In addition, our results also suggest that methanol extract of Hedyotis diffusa reduces the malignant potential of HL-60 cells via down regulation of colony forming effciency through cleavage of Bc12 as well as induction of Bax.

• Journal of Animal Science and Technology
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• v.49 no.6
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• pp.729-736
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• 2007

The objective of this study was to investigate the anti-oxidative effects of pyruvate, taurine and melatonin on sperm characteristics(motility, membrane integrity) and lipid peroxidation(LPO) for in vitro storage of boar semen. Semen was treated with various antioxidants such as pyruvate(1mM), taurine(50mM) and melatonin(100nM) with or without 100uM H2O2. Antioxidant treatments were significantly increased the sperm motility when compare to control group in all incubation periods(P≤0.05). Hypoosmotic swelling test(HOST), membrane integrity was similar to the result of motility. In lipid peroxidation measurement by TBA reactions of spermatozoal plasma membrane, malondialdehyde(MDA) level in control and antioxidant treatments were lower than those of antioxidant plus H2O2 or H2O2 treatment for 3 to 6 h incubation period. Relationships of evaluation methods for sperm viability were investigated by motility, membrane integrity and lipid peroxidation. Among evaluation methods, LPO vs motility and membrane integrity vs LPO were negatively correlated(－0.23~－0.92 and －0.68~－0.85), but membrane integrity vs motility was positively correlated (0.53~0.94) in all treatments. These experiments indicate that supplementation of antioxidant to the semen extender can increase the sperm motility and membrane integrity and decrease the lipid peroxidation of spermatozoal plasma membrane. The HOST might be utilized to evaluate the sperm quality instead of lipid peroxidation or motility.

• Journal of Life Science
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• v.27 no.10
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• pp.1215-1224
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• 2017

Until now, various oncogenic pathways were idenfied. The accumulation of DNA mutation induces genomic instability in the cell, and it makes cancer. The development of bioinformatics and genomics, to find the precise and reliable biomarker is available. This biomarker could be applied the early-dignosis, prediction and convalescence of cancer. Recently, Transposable elements (TEs) have been attracted as the regulator of genes, because they occupy a half of human genome, and the cause of various diseases. TEs induce DNA mutation, as well as the regulation of gene expression, that makes to cancer development. So, we confirmed the relationship between TEs and colon cancer, and provided the clue for colon cancer biomarker. First, we confirmed long interspersed nuclear element-1 (LINE-1), Alu, and long terminal repeats (LTRs) and their relationship to colon cancer. Because these elements have large composition and enormous effect to the human genome. Interestingly, colon cancer specific patterns were detected, such as the hypomethylation of LINE-1, LINE-1 insertion in the APC gene, hypo- or hypermethylation of Alu, and isoform derived from LTR insertion. Moreover, hypomethylation of LINE-1 in proto-oncogene is used as the biomarker of colon cancer metastasis, and MLH1 mutation induced by Alu is detected in familial or hereditary colon cancer. The genes, effected by TEs, were analyzed their expression patterns by in silico analysis. Then, we provided tissue- and gender-specific expression patterns. This information can provide reliable cancer biomarker, and apply to prediction and diagnosis of colon cancer.

• Korean Journal of Poultry Science
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• v.43 no.4
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• pp.273-279
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• 2016

Recently, it was reported that certain polymorphisms in the growth hormone secretagogue receptor gene (GHSR) are associated with the growth of chickens. However, the correlation between GHSR polymorphisms and economic traits has not been investigated in Korean native chickens (KNCs). Therefore, the objective of this study was to confirm the suitability of the GHSR gene as a candidate for genomic selection and identify a genetic marker for KNCs. A total of 220 KNCs from six breeds raised at the National Institute of Animal Science were genotyped for the c.739+726 SNP in the GHSR gene using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP), and the sequence for a subset of 30 birds was analyzed using direct sequencing. The association between the SNP genotypes and the economic traits of the KNCs was analyzed using the statistical package for the social science (SPSS) software program. The association analysis between the c.739+726T>C SNP and economic traits revealed that the SNP was significantly associated with body weight at 150 and 270 days (BW150 and BW270, respectively) in all KNCs (p<0.01), BW150 in KNC (Gary) (p<0.05), and egg production number in KNC (White, p<0.05). In addition, the SNPs discovered using direct sequencing (513A>G, 517A>T) had a significant effect on the body weight and egg production traits (p<0.05). In conclusion, these results might be useful as a basis for studies on the improvement of KNC breeds. Furthermore, these results suggest that the SNPs (c.739+726T>C, 513A>G, and 517A>T) located in the GHSR gene could be useful molecular genetic markers for KNCs.

• Tuberculosis and Respiratory Diseases
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• v.60 no.4
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• pp.451-463
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• 2006

Background : Reactive oxygen species (ROS) take center stage as executers in ventilator-induced lung injury (VILI). The protein with DNA-damage scanning activity, poly (ADP-ribose) polymerase-1 (PARP1), signals DNA rupture and participates in base-excision repair. Paradoxically,overactivation of PARP1 in response to massive genotoxic injury such as ROS can induce cell death through ${\beta}$ -nicotinamide adenine dinucleotide ($NAD^+$) depletion, resulting in inflammation. The purpose of this study is to investigate the role of PARP1 and the effect of its inhibitor in VILI. Methods : Forty-eight male C57BL/6 mice were divided into sham, lung protective ventilation(LPV), VILI, and PARP1 inhibitor (PJ34)+VILI (PJ34+VILI) groups. Mechanical ventilator setting for the LPV group was $PIP\;15cmH_2O$ + $PEEP\;3cmH_2O$ + RR 90/min + 2 hours. The VILI and PJ34+VILI groups were ventilated on a setting of $PIP\;40cmH_2O$ + $PEEP\;0cmH_2O$ + RR 90/min + 2 hours. As a PARP1 inhibitor for the PJ34+VILI group, 20 mg/Kg of PJ34 was treated intraperitoneally 2 hours before mechanical ventilation. Wet-to-dry weight ratio and acute lung injury (ALI) score were measured to determine the degree of VILI. PARP1 activity was evaluated by using an immunohistochemical method utilizing biotinylated NAD. Myeloperoxidase (MPO) activity and the concentration of inflammatory cytokines such as tumor necrosis factor $(TNF)-{\alpha}$, interleukin $(IL)-1{\beta}$, and IL-6 were measured in bronchoalveolar lavage fluid (BALF). Results : In the PJ34+VILI group, PJ34 pretreatment significantly reduced the degree of lung injury, compared with the VILI group (p<0.05). The number of cells expressing PARP1 activity was significantly increased in the VILI group, but significantly decreased in the PJ34+VILI group (p=0.001). In BALF, MPO activity, $TNF-{\alpha}$, $IL-1{\beta}$, and IL-6 were also significantly lower in the PJ34+VILI group (all, p<0.05). Conclusion : PARP1 overactivation plays a major role in the mechanism of VILI. PARP1 inhibitor prevents VILI, and decreases MPO activity and inflammatory cytokines.