• Genomics & Informatics
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• v.18 no.4
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• pp.42.1-42.9
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• 2020

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

• Korean Journal of Agricultural Science
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• v.24 no.1
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• pp.11-15
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• 1997

The importance value and volume growth percentage, based on the data obtained from 33 quadrats by $relev{\acute{e}}$ method of Mueller-Dombois and Ellenberg, were applied to investigate Pinus thunbergii forests in Taean Haean National Park. The investigation was done from July till September 1996. 1. The dominant species of tree were found in the order of Pinus thunbergii, Quercus dentata, Robinia pseudcacacia, Platycarya strobilacea, Carpinus coreana, Albizzia julibrissin, Pinus densi-thunbergii, and Quercus serrata 2. The volume growth percentage of Pinus thunbergii was about 0.6%~10.5% and the mean of it's was 3.8%. 3. Chemical properties of forest soil showed ranging pH 4.8~6.3, organic matter 1.51~11.79%, $P_2O_5$ 2.5~14.5ppm, $Ca^{{+}{+}}$ 1.3~6.6(me/100g), $Mg^{{+}{+}}$ 0.4~2.6(me/100g), and $K^+$ 0.23~1.89(me/100g).

• Journal of Animal Science and Technology
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• v.63 no.5
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• pp.984-997
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• 2021

This study sought to evaluate DNA damage and repair in porcine postovulatory aged oocytes. The DNA damage response, which was assessed by H2A.X expression, increased in porcine aged oocytes over time. However, the aged oocytes exhibited a significant decrease in the expression of RAD51, which reflects the DNA damage repair capacity. Further experiments suggested that the DNA repair ability was suppressed by the downregulation of genes involved in the homologous recombination (HR) and nonhomologous end-joining (NHEJ) pathways. The expression levels of the cell cycle checkpoint genes, CHEK1 and CHEK2, were upregulated in porcine aged oocytes in response to induced DNA damage. Immunofluorescence results revealed that the expression level of H3K79me2 was significantly lower in porcine aged oocytes than in control oocytes. In addition, embryo quality was significantly reduced in aged oocytes, as assessed by measuring the cell proliferation capacity. Our results provide evidence that DNA damage is increased and the DNA repair ability is suppressed in porcine aged oocytes. These findings increase our understanding of the events that occur during postovulatory oocyte aging.

• Journal of Embryo Transfer
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• v.20 no.2
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• pp.137-145
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• 2005

본 연구는 NCSU-23과 PZM-3 배양액에 EGF, $\beta-ME$와 glucose의 첨가가 돼지 난자의 체외성숙에 미치는 영향과, 배양조건을 다르게 하여 계대배양한 섬유아세포를 이용한 핵이식 배를 다른 배양액과 산소조건에서 배양하였을 때 체외발생율에 미치는 영향을 조사하였다. 난자를 20ng/ml EGF를 첨가 또는 첨가하지 않은 NCSU-23 및 PZM-3 배양액에서 44시간 배양하였을 때 난자의 체외성숙율은 각각 $85.7\pm3.1\%,\;75.2\pm2.8\%,\;87.1\pm2.4\%$와 $78.2\pm2.6\%$였으며 EGF를 첨가한 배양액에서 배양한 난자의 체외성숙율은 EGF를 첨가하지 않은 배양액에서 배양했을 때의 난자보다 높은 체외성숙율을 나타냈다(p<0.05). 난자를 $25{\mu}M\;\beta-ME$를 첨가 또는 첨가하지 않은 NCSU-23 및 PZM-3 배양액에서 44시간 배양하였을 때 난자의 체외성숙율은 각각 $79.5\pm2.6\%,\;74.7\pm2.5\%,\;80.2\pm2.3\%,\;78.6\pm2.7\%$였고 $\beta-ME$를 첨 가한 PZM-3 배양액에서 배양한 난자의 체외성숙율이 가장 높게 나타났다. 난자를 1.5mM glucose를 첨가 또는 첨가하지 않은 NCSU-23 및 PZM-3 배양액에서 44시간 배양하였을 때 난자의 체외성숙율은 각각 $79.2\pm2.3\%,\;75.0\pm2.6\%,\;85.5\pm2.5\%$와 $78.9\pm2.7\%$였고, glucose를 첨가한 PZM-3 배양액에서 배양한 난자의 체외성숙율은 glucose를 첨가하지 않은 PZM-3 배양액에서 배양한 난자보다 높은 체외성숙율을 나타냈다(p<0.05). 핵이식 배를 20ng/m1 EGF, $25{\mu}M\;\beta-ME$ 및 1.5mM glucose를 첨가한 NCSU-23 및 PZM-3 배양액에서 48시간, 144시간 배양하였을 때 2세포기 및 배반포로의 체외발생율은 각각 $56.4\pm2.7\%,\;54.3\pm2.9\%,\;70.5\pm2.1\%,\; 69.6\pm1.5\%$ 및 $12.0\pm1.3\%,\;9.6\pml.7\%,\;10.9\pm2.1\%,\;11.9\pm1.8\%$였다.

• Korean Journal of Soil Science and Fertilizer
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• v.6 no.4
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• pp.205-211
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• 1973

General physical and chemical characteristics of eleven apple orchard soils derived from granite, granodiorite, diorite, arkose sandstone and shale were investigated in relation to soil profile. The results are summerized as follows: 1. Soils were mostly sandy and showed pH 4.35 to 6.75, 1.14 to 5.58 of organic matter, 0.065 to 0.209% of nitrogen. All properties decreased with depth. 2. Total exchangeable bases of surface soils were comparablly low (4.89 to 17.81me/100g, Ca>Mg>K>Na). Cation exchange capacity ranged from 7.74 to 21.72 mg/100g and base saturation percentage from 22.52 to 94.62%. 3. Phosphorus content of surface soil was very low (less than 35.5 mg/100g). The contents of potassium (7.2-79.2 mg/100g), available copper (1.0-16.9 ppm) and water soluble boron (0.18-0.72 ppm) were high in surface soil but low with depth. The content of manganese showed clear difference with pH, that is, at pH 4 to 6 water soluble manganese ranged from 0.42 to 17.8 ppm and exchangeable manganese from 9.82 to 66.38 ppm but above pH 6 the water soluble was less than 0.70 ppm and the exchangeable less than 22.25 ppm.

• Food Science and Preservation
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• v.24 no.3
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• pp.431-439
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• 2017

This study was conducted to examine the antioxidant activities and physiological activities of mixture extracts (Liriope platyphylla, Schizandra chinensis and Panax ginseng C.A. Meyer) with different extraction mixing ratios (MEC, 2:1:1; ME1, 1:2:1; ME2, 1:1:2; ME3, 1.34:1.33:1.33). The yield of extracts ranged from 25.33 to 33.87%. The total polyphenol and total flavonoid contents of ME1 extracts were 1.01 g/100 g, 0.07 g/100 g, respectively. The total sugar contents of MEC extract was 22.83 g/100 g, respectively. The DPPH and ABTS radical scavenging activities of ME1 extracts at $1,000{\mu}g/mL$ were 26.79% and 21.08%. The superoxide radical scavenging and ferric-reducing antioxidant power of ME1 extracts at $1,000{\mu}g/mL$ were 67.83% and $295.47{\mu}M$, respectively. The functionalities of extracts were investigated with L-132 and RAW264.7 cell lines. The extracts on different mixing ratios did not show the toxicity on L-132 and RAW264.7 cell line in $100-2,500{\mu}g/mL$. The ME1 extract of $1,000{\mu}g/mL$ performed better than other extracts protective effects against oxidative stess in L-132 cells (81.22%) and the ME2 extract at $1,000{\mu}g/mL$ decreased nitric oxide production by $7.48{\mu}M$ which was more potent than other extracts. There results suggest that the ME1 extracts may be a useful functional food material in the food industry.

• Nuclear Engineering and Technology
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• v.38 no.5
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• pp.405-410
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• 2006

Microstructural features and their related mechanical property changes in the 309L cladding and the heat affected zone (HAZ) of SA508 cl.3 steel were investigated through the use of TEM, tensile and small punch (SP) tests. The specimens were irradiated at 563 K up to the neutron fluences of $5.79{\times}10^{19}n/cm^2$ (>1MeV). The microstructure of the clad was mainly composed of a fcc ${\gamma}-phase$, a low percentage of bcc ${\delta}-ferrite$, and a brittle ${\sigma}-phase$. Along the weld fusion line there formed a heavy carbide precipitation with a width of $20{\sim}40{\mu}m$, showing preferential cracking during plastic deformation. The yield stress and ductile-to-brittle transition temperature (DBTT) of the irradiated clads increased. The origin of the hardening and the shift of the DBTT are discussed in terms of the irradiation-produced defect clusters of a fine size and brittle ${\sigma}-phase$.

• Applied Biological Chemistry
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• v.15 no.2
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• pp.169-173
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• 1972

In five varietes of Citrus junos sieb grown in different area in Korea, the general components, total acids and inorganic components were calculated and compared with one other. In the orchard soils, the physical and chemical properties were studied. The results are summarized as follow: 1. Generally, the rind was weighter than tile flesh compared with the other fruits and the proportion of the rind was 49%. 2. Total contents of organic acids in rind and flesh were 12.29me and 39.79me respectively. 3. The order of the contents of inorganic components in the flesh and rind was $CaO>K_2O>MgO>P_2O_5>SO_4$ 4. The contents of crude protein and crude fat were increased with those of MgO and $SO_4$ in fruits. 5. The quantity of protein in the soil seed to influence greatly in rind formation not only in citrus fruits but also Citrus junos sieb. 6. In growing Citrus junos sieb, C.L. seemed to he the most adequate soil. 7. The pH range of the soil was from 5.05 to 7.20 generally. 8. The contents of crude protein and crude fat in citrus fruits seemed to be increased with those of organic material and total-nitrogen in the soil.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.3
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• pp.386-391
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• 2017

Objective: Protein supplementation is costly and can result in excess nitrogen (N) excretion. The objective of this study was to evaluate the effects of feeding different levels of dietary protein on average daily gain, body size, rumen fermentation, and nitrogen excretion of 8 to 10 month-old Holstein heifers. Methods: Thirty-six Holstein heifers were divided into 12 blocks according to age ($273{\pm}6.2d$) and were randomly assigned to diets containing a low (10.2% dry matter [DM]), medium (11.9% DM), or high (13.5% DM) level of dietary crude protein (CP). All diets contained approximately 70% roughage and 30% concentrate with similar dietary metabolizable energy (ME) content (2.47 Mcal/kg). Results: Dry matter intake did not differ among the treatments, and average daily gain increased with the increasing dietary protein, 0.79, 0.95, 0.97 kg/d for low, medium, and high group, respectively. Body height increased linearly with increasing dietary CP but no other significant differences in body dimensions were found among the treatments. The increased ratios of dietary CP improved the rate of rear teat length growth remarkably (p<0.05). There was no difference in rumen pH or ruminal major volatile fatty acid (acetate, propionate, and butyrate) concentration among the 3 diets, but rumen ammonia-N concentration increased with the higher dietary CP (p<0.05). Increasing N intake led to increased total N excretion; urinary N excretion was significantly increased (p<0.05) but fecal N excretion was similar among the treatments. Conclusion: These data suggest that the diet containing 11.9% CP (ME 2.47 Mcal/kg) could meet the maintenance and growth requirements of 9 to 11 month-old Holstein heifers gaining approximately 0.9 kg/d.

• Journal of dental hygiene science
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• v.10 no.5
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• pp.365-372
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• 2010

Caesalpinia sappan L. has long been commonly used in oriental folk medicines and as dyes materials. To investigate the antioxidative activities and antiproliferation effects of brazilin from C. sappan heart wood, the MeOH soluble extract was successively fractionated by using hexane, $CHCl_{3}$, EtOAc, BuOH, MeOH, and $H_{2}O$. In these fractions, we were purified brazilin from EtOAc fraction which partitioned to 3.94% of the highest yields. The effects of brazilin and the extracts on human oral carcinoma cells (KB) by MTT assay and their antioxidant activities by DPPH, TCA assay and Fenton reaction were tested. The results showed that the brazilin could inhibits the proliferation of KB cells and obviously decreased the production of nitric oxide of the cells. When the concentration of the brazilin reached to $100\;{\mu}g/ml$, the inhibition percentage of the cell growth was about 60%. In assay on antioxidant activities, The results showed that brazilin exhibit the highest capacity of DPPH free radical scavenging effects among tested extracts. When the concentration of brazilin reached to 1 mg/ml, the lipid peroxide inhibition and radical inhibition activities were determined to be 65.0% and 85.8%, respectively. These results are suggest that brazilin have stronger antiproliferation effect on KB cell and antioxidant properties.