• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.84-84
• /
• 2017

Eleutherococcus senticosus (Siberian ginseng) is an important medicinal tree found in Russian taiga, and northern regions of Korea, Japan, and China. In this study, we analyzed the genome-wide distribution of microsatellites in E. senticosus using developed SSR markers. A total of 711 clones from an SSR-enriched genomic DNA library were sequenced, of which 47 clones (6.6%) were redundant. Of the 664 independent clones, only 12 polymorphic SSR markers were obtained, which also revealed successful amplicons in E. senticosus accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 131 E. senticosus accessions in Korea and China. The number of alleles ranged from 2 to 11, with an average of 7.4 alleles. The mean values of observed heterozygosity ($H_O$) and expected heterozygosity ($H_E$) were 0.59 and 0.56, respectively. The average polymorphism information content (PIC) was 0.51 in all 131 E. senticosus accessions. E. senticosus accessions in Korea and China showed a close genetic similarity. Significantly low pairwise genetic divergence was observed between the two regions, suggesting a relatively narrow level of genetic basis among E. senticosus accessions. Our results not only provide molecular tools for genetic studies in E. senticosus but are also helpful for conservation and E. senticosus breeding programs.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.113-113
• /
• 2017

Downy mildew (DM), caused by several species in the Peronosclerospora and Scleropthora genera, is a major maize (Zea mays L.) disease in tropical or subtropical regions. DM is an obligate parasite species in the higher plants and spreads by oospores, wind, and mycelium in seed surface, soil, and living hosts. Owing to its geographical distribution and destructive yield reduction, DM is one of the most severe maize diseases among the maize pathogens. Positional cloning in combination with phenotyping is a general approach to identify disease resistant gene candidates in plants; however, it requires several time-consuming steps including population or fine mapping. Therefore, in the present study, we suggest a new combination strategy to improve the identification of disease resistant gene candidates. Downy mildew (DM) resistant maize was selected from five cultivars using the spreader row technique. Positional cloning and bioinformatics tools identified the DM resistant QTL marker (bnlg1702) and 47 protein coding genes annotations. Eventually, 5 DM resistant gene candidates, including bZIP34, Bak1, and Ppr, were identified by quantitative RT-PCR without fine mapping of the bnlg1702 locus. Specifically, we provided DM resistant gene candidates with our new strategy, including field selection by the spreader row technique without population preparation, the DM resistance region identification by positional cloning using bioinformatics tools, and expression level profiling by quantitative RT-PCR without fine mapping. As whole genome information is available for other crops, we propose applying our novel protocol to other crops or for other diseases with suitable adjustment.

• Journal of Plant Biotechnology
• /
• v.46 no.4
• /
• pp.255-273
• /
• 2019

Orchids are indispensable to the floriculture industry due to their unique floral organization. The flowers have two outer whorls of tepals including a lip (labellum), and two inner whorls, pollinia and gynostemiun (column). The floral organization and development is controlled at the molecular level, mainly by the MADS-box gene family, comprising homeotic genes divided into type I and type II groups. The type I group has four sub-groups, Mα, Mβ, Mγ, and Mδ, playing roles in seed, embryo, and female reproductive organ development; the type II group genes form classes A, B, C, D, and E, which are a part of the MIKC^C subgroup with specific roles in florigenesis and organization. The coordinated functioning of these classes regulates the development of various floral whorls. The availability of genome and transcriptome sequence data for Phalaenopsis equestris offers an opportunity to validate the ABCDE model of flower development. Hence, this study sought to characterize the MADS-box gene family and elucidate of the ABCDE model. A total of 48 identified MADS-box proteins, including 20 type I [Mα (12), Mγ (8)] and 28 type II [MIKC^C (27), MIKC*(1)] members, were characterized for physico-chemical features and domains and motifs organization. The exon-intron distribution and the upstream cis-regulatory elements in the promoter regions of MADS-box genes were also analysed. The discrete pace of duplication events in type I and type II genes suggested differential evolutionary constraints between groups. The correlation of spatio-temporal expression pattern with the presence of specific cis-regulatory elements and putative protein-protein interaction within the different classes of MADS-box gene family endorse the ABCDE model of floral development.

• Animal Systematics, Evolution and Diversity
• /
• v.28 no.4
• /
• pp.279-290
• /
• 2012

Plecoglossus altivelis (ayu) is an amphidromous fish widely distributed in Northeastern Asia from the East China Sea to the northern Japanese coastal waters, encompassing the Korean Peninsula within its range. The shore lines of northeastern region in Asia have severely fluctuated following glaciations in the Quaternary. In the present study, we investigate the population genetic structure and historical demographic change of P. altivelis at a population level in East Asia. Analysis of molecular variance (AMOVA) based on 244 mitochondrial control region DNA sequences clearly showed that as the sampling scope extended to a larger geographic area, genetic differentiation began to become significant, particularly among Northeastern populations. A series of hierarchical AMOVA could detect the genetic relationship of three closely located islands between Korea and Japan that might have been tightly connected by the regional Tsushima current. Neutrality and mismatch distribution analyses revealed a strong signature of a recent population expansion of P. altivelis in East Asia, estimated at 126 to 391 thousand years ago during the late Pleistocene. Therefore it suggests that the present population of P. altivelis traces back to its approximate demographic change long before the last glacial maximum. This contrasts our a priori expectation that the most recent glacial event might have the most crucial effect on the present day demography of marine organisms through bottleneck and subsequent increase of effective population size in this region.

• Journal of Korean Society of Water and Wastewater
• /
• v.13 no.2
• /
• pp.66-73
• /
• 1999

This study was carried out to derive the removal characteristics of target materials(DOC and turbidity) during the coagulation process after the injection of coagulants(PACl and FeCl3). Used apparatus were a jar test and a pilot plant. A great portion of DOC among the total removed DOC was achieved at the slow mixing process among the coagulation process. The ranges of removed DOC and optimum pH for each coagulant were 0.45~1.47mg/l and 6.0~6.5 by PACl, and 0.97~2.61mg/l. and 5.0~5.5 by FeCl3, respectively. Both of coagulants showed little increase of DOC removal above coagulant dosage 20mg/l Molecular weight distribution(MWD) of removed DOC was measured by get filtration(GF) technique. The MWD variation by gel filtrationin(GF) for removed DOC in the coagulation process were as follows; for raw water, the percentages of each MWD for total area were < MW 6,500 25.5%, MW 6,500~66,000 67.1%, and > MW 66,000 7.4%. For the same coagulant dosage(12mg/l), the percentages of each MWD for total area by PACl were < MW 6,500 20.5%, MW 6,500~66,000 48.7%, and > MW 66,000 9.1%, and those of FeCl3 were MW 66,000 18.2%. For each coagulant, the removal percentage of MW 6,500~66,000 occurred a little, but at a part of

• Journal of Korean Society of Water and Wastewater
• /
• v.32 no.5
• /
• pp.389-398
• /
• 2018

A nationwide survey of 8 N-nitrosamines in finished water samples from drinking water treatment plants (DWTPs) in Korea was conducted. The samples were pre-treated by solid-phase extraction (SPE) and analyzed using a gas chromatography coupled with tandem mass spectrometry (GC-MS/MS). According to the study results, four N-nitrosamines (NDMA, NDEA, NMOR, NDBA) were detected for three consecutive years, NMEA and NPYR were only found in samples collected in 2013. Two of these N-nitrosamines, N-nitrosodimethylamine (NDMA) and N-nitrosodiethylamine (NDEA), have received attention and were the most commonly detected. The concentration of NDMA and NDEA in this study ranged from $0.002{\mu}g/L$ to $0.013{\mu}g/L$ and in $0.001{\mu}g/L$ to $0.008{\mu}g/L$, respectively. In comparison to studies performed in EPA(UCMR2), the concentrations of NDMA (from $0.002{\mu}g/L$ to $0.630{\mu}g/L$) and NDEA (from $0.005{\mu}g/L$ to $0.100{\mu}g/L$) observed in the this study were low.

• Asian-Australasian Journal of Animal Sciences
• /
• v.23 no.2
• /
• pp.272-278
• /
• 2010

In this study, we cloned, sequenced and characterized porcine y+L Amino Acid Transporter-1 (y+LAT1). By screening a translated EST database with the protein sequence of the human $y^{+}$LAT1 and by using rapid amplification of cDNA ends (RACE), the full-length cDNA encoding porcine $y^{+}$LAT1 was isolated from porcine intestine RNA. It was 2,111 bp long, encoding a 511 amino acid trans-membrane glycoprotein composed of 12 transmembrane domains. The predicted amino acid sequence was found to be 91%, 90%, 87% and 87% identical to those of cattle, human, mouse and rat $y^{+}$LAT1 respectively. Real-time RT-PCR results indicated that the small intestine had the highest $y^{+}$LAT1 mRNA abundance and the lung had the lowest $y^{+}$LAT1 mRNA abundance. Baby hamster kidney (BHK) cells transfected with green fluorescent protein (GFP) tagged porcine $y^{+}$LAT1 cDNA indicated that the cellular localization of the gene product in BHK was on the plasma membrane.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.9
• /
• pp.1393-1400
• /
• 2018

Objective: This study was carried out to assess the haplotype diversity and population dynamics in cattle populations of Ethiopia. Methods: We sequenced the complete mitochondrial cytochrome b gene of 76 animals from five indigenous and one Holstein Friesian${\times}$Barka cross bred cattle populations. Results: In the sequence analysis, 18 haplotypes were generated from 18 segregating sites and the average haplotype and nucleotide diversities were $0.7540{\pm}0.043$ and $0.0010{\pm}0.000$, respectively. The population differentiation analysis shows a weak population structure (4.55%) among the populations studied. Majority of the variation (95.45%) is observed by within populations. The overall average pair-wise distance ($F_{ST}$) was 0.049539 with the highest ($F_{ST}=0.1245$) and the lowest ($F_{ST}=0.011$) $F_{ST}$ distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. No haplotype in Ethiopian cattle was observed clustered with the reference Bos indicus group. The mismatch distribution analysis indicates a single population expansion event among the cattle populations. Conclusion: Overall, high haplotype variability was observed among Ethiopian cattle populations and they share a common ancestor with Bos taurus.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.7
• /
• pp.3471-3476
• /
• 2012

Background and Objective: Histone deacetylase (HDAC) inhibitors represent a promising class of potential anticancer agents for treatment of human malignancies. In this study, we investigated the effect of trichostatin A (TSA), one such HDAC inhibitor, in combination with docetaxel (TXT), a cytotoxic chemotherapy agent or erlotinib, a novel molecular target therapy drug, on lung cancer A549 cells. Methods: A549 cells were treated with TXT, erlotinib alone or in combination with TSA, respectively. Cell viability, apoptosis, and cell cycle distribution were evaluated using MTT (3- (4, 5-dimethylthiazol-2-yl) -2, 5-diphenyltetrazolium bromide) assay, Hochst33258 staining and flow cytometry. Moreover, immunofluorescent staining and Western blot analysis were employed to examine alterations of ${\alpha}$-tubulin, heat shock protein 90 (hsp90), epidermal growth factor receptor (EGFR), and caspase-3 in response to the different exogenous stimuli. Results: Compared with single-agent treatment, co-treatment of A549 cells with TSA/TXT or TSA/erlotinib synergistically inhibited cell proliferation, induced apoptosis, and caused cell cycle delay at the $G_2/M$ transition. Treatment with TSA/TXT or TSA/erlotinib led to a significant increase of cleaved caspase-3 expression, also resulting in elevated acetylation of ${\alpha}$-tubulin or hsp90 and decreased expression of EGFR, which was negatively associated with the level of acetylated hsp90. Conclusions: Synergistic anti-tumor effects are observed between TXT or erlotinib and TSA on lung cancer cells. Such combinations may provide a more effective strategy for treating human lung cancer.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.8
• /
• pp.3507-3511
• /
• 2014

Background: The prostaglandin-endoperoxide synthase 2 [PTGS2, commonly known as cyclooxygenase-2 (COX-2)] is an enzyme induced by proinflammatory stimuli that is often overexpressed in malignant tissue and involved in the synthesis of prostaglandins and thromboxanes, regulators of processes such as inflammation, cell proliferation, and angiogenesis, all relevant for cancer development. We investigated whether a functional genetic polymorphism, rs5277, in COX-2 may have a risk-modifying effect on sporadic colorectal cancer in an Iranian population. Materials and Methods: We conducted a case-control study on 167 patients with colorectal cancer and 197 cancer-free controls in Taleghani Hospital in Tehran, Iran, between 2007 and 2011. Peripheral blood samples of both groups were processed for DNA extraction and genotyping of the COX-2 gene polymorphism (rs5277) using PCR-RFLP. RFLP results were confirmed by direct sequencing. Logistic regression analysis was performed to calculate the adjusted odds ratio (OR) and 95% confidence interval (95% CI). Results: There was no significant difference in the distribution of COX-2 gene rs5277 polymorphism genotype and the allelic form, among CRC patients compared with the healthy control group (p: 0.867). Conclusions: Our results suggest that rs5277 polymorphism in COX2 could not be a good prognostic indicator for patients with CRC.