• Journal of Korean Society of Forest Science
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• v.90 no.1
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• pp.155-160
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• 2001

Changes in genetic diversity after seed-tree practice were simulated in test plantation of tulip tree at Sokdal-ri, Banwol-myon, Hwasung-gun, Kyungki Provence. I-SSR markers were analyzed in a total of 305 tulip trees. A total of 89 amplicon variants were observed by PCR with 9 I-SSR primers. Genetic diversity for 305 trees was relatively high (S. I. =0.4532). Individuals originated from the seed orchards in U.S.A. showed the highest level of genetic diversity (0.4530), those from Anyang showed the medium level (0.4152), and those from Cheonbuk showed the lowest (0.3929). Simulation of seed-tree practice accompanied by 2 consecutive thinnings was performed on the basis of morphological characteristics and planted distances of the individual trees, which left 37 trees as candidates for seed-trees. Decreasing rate of genetic diversity within seed sources was greatest for individuals from Cheonbuk (28.3%), moderate for those from Anyang (16.3%), and smallest for those from U.S.A. (8.0%). In spite of little difference in decreasing rate of individuals for the 3 seed sources (87.5~88.2%), large difference in decreasing rate of genetic diversity within seed sources might be due to difference in number of mother trees for the 3 seed sources. For example, whereas individuals originated from the seed orchard in U.S.A., which showed the smallest decreasing rate of genetic diversity, might be originated from relatively large number of mother trees, those from Anyang and Cheonbuk might be originated from relatively small number of mother trees. Although mean of 17.5% of the genetic diversity within seed sources was decreased through 2 consecutive thinnings, a decrease in genetic diversity for the whole individuals (37 trees) was only 6.1%. This observation suggests that the seed-tree practice on the basis of the criteria established in the present study may not result in great reduction in overall genetic diversity of the progenies.

• Journal of Applied Biological Chemistry
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• v.66
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• pp.416-423
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• 2023

Figs has known to have antioxidant, whitening, anti-inflammatory, and antibacterial effects in their leaves, roots, stems, latex, and fruits. In order to develop cosmetic materials based on natural products, we have studied on the skin activity of the ficin in latex as well as the whitening function of the fruit extract with 70% ethanol, and used it as a raw material for released cosmetic product. However, there is little research on the demand for the development of new eutectic solvent extraction methods and its ability to control skin inflammation and psoriasis regulation. Thus, in this study, we evaluated the effectiveness of fig fruit extracts and fractions using eutectic solvent extraction for skin inflammation control and psoriasis. First, fig fruits were extracted under optimal eutectic solvent conditions and fractionated with n-hexane, dichloromethane, ethyl acetate, and butanol. First, the antioxidant activity and inhibition of nitric oxide (NO) production were confirmed in mouse macrophage RAW264.7 cells. In addition, as a result of observing the mRNA expression through RT-PCR, pro-inflammatory cytokines such as TNF-α, IL1α, and IL-1β were suppressed significantly in the hexane, dichloromethane, and ethyl acetate fractions. In addition, it was confirmed in TNF-α stimulated HaCaT keratinocyte model. Finally, chemokine CC motif ligand 20 (CCL20), marker gene of human psoriasis skin disease, was significantly suppressed in the hexane, dichloromethane, and ethyl acetate fractions. These results suggested its anti-inflammatory and skin soothing effect and the possibility of development as an excellent skin soothing natural cosmetic material in the future through future clinical trials.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.3
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• pp.199-213
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• 2020

Grain size and shape are the two important components contributing to rice yield and quality. To analyze traits related to grain-shape, a total of 272 varieties derived from japonica, japonica black and Tongil-type rice accession in Korea were evaluated in this study. The traits, grain length (GL), grain width (GW), grain thickness (GT), length to width ratio (RLW), and 1000-grain weight (TGW) were measured and replicated 10 times. Genes (GW2, GS3, qGL3, qSW5, GS5, TGW6, GW7, and GW8) related to grain-shape were validated in the accessions using specific DNA marker sets. K-mean clustering of the accession based on phenotypic data revealed three groups: group 1 was classified by GW and GT and included most of japonica type, group 2 was classified by RLW and GL reached a medium size and possessed a half spindle-shaped type, and group 3 was classified by TGW, reached a long size and possessed a semi-round shape. In validation tests using the marker sets, both gw2 and tgw6 were validated in less than 1% of the tested accessions and two allelic types, qgl3 and gw8, were only verified in Tongil-type accessions. For GW8 and GW2, any different amplicons were not amplified in any japonica or Tongil-type accessions, respectively. In order to suggest the representative grain-shape gene combinations for each ecotype, the allelic combinations were evaluated by PCR analysis. Cj1 and 2 in japonica (Cj1-7), Cj_b1 and 2 in japonica-black (Cj_b1-3), and CT3 in Tongil-type (CT1-13) turned out to be the dominant combination in each ecotype, respectively. In addition, the results revealed that introgression of four genes (gw2, gs3, qSW5, and GS5) would expand the diversity of grain shape in Korean japonica varieties. The gene combinations information could be utilized practically to understand or enhance grain shape in japonica rice breeding program.

• Journal of Chest Surgery
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• v.37 no.12
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• pp.967-977
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• 2004

Background: DNA methylation is one of the important gene expression mechanisms of the cell. When cytosine of CpG dinucleotide in promotor is hypomethylated, expression of some genes that is controlled by this promoter is altered. In this study, the author investigated the effect of DNA demethylating agent, 5-aza-2'-deoxycytidine (ADC), on the expressions of cancer antigen genes, MHC and B7 in 4 lung cancer cell lines, NCIH1703, NCIH522, MRC-5, and A549. Material and Method: After treatment of cell lines, NCIH1703, NCIH522, MRC-5 and A549 with ADC (1 uM) for 48 hours, RT-PCR was performed by using the primers of MAGE, GAGE, NY-ESO-1, PSMA, CEA, and SCC antigen gene. In order to find the optimal ADC treatment condition for induction of cancer antigen, we studied the effect of ADC treatment time and dose on the cancer antigen gene expression. To know the effect of ADC on the expression of MHC or B7 and cell growth, cells were treated with 1 uM of ADC for 72 hours for FACS analysis or cells were treated with 0.2, 1 or 5 uM of ADC for 96 hours for cell counting. Result: After treatment of ADC (1 uM) for 48 hours, the expressions of MAGE, GAGE, NY-ESO-1, and PSMA genes increased in some cell lines. Among 6 MAGE isotypes tested, and gene expression of MAGE-1, -2, -3, -4 and -6 could be induced by ADC treatment. However, CEA gene expression did not change and SCC gene expression was decreased by ADC treatment. Gene expression was generally induced 24 - 28 hours after ADC treatment and expression of MAGE, GAGE, and NY-ESO-1 was maintained at least 14 days after ADC ADC teatment, and expression of MAGE, GAGE, and NY-ESO-1 was maintained at least 14 days after ADC teatment in ADC-Free medium. Most gene expression could be induced at 0.2 uM of ADC, but gene expression increased dependently on ADC treatment dose. The expression of MHC and B7 was not increased by ADC treatment in all four cell lines, and the growth rate of 4 cell lines decreased significantly with the increase of ADC concentrations. Conclusion: Treatment of lung cancer cell lines with ADC increases the gene expression MAGE, GAGE and NY-ESO-1 that are capable of induction of cytotoxic T lymphocyte response. We suggest that treatment with 1 uM of ADC for 48 hours and then culturing in ADC-free medium is optimal condition for induction of cancer antigen. However, ADC has no effect on MHC and B7 induction, additional modification for increase of expression of MHC, B7 and cytokine will be needed for production of efficient cancer cell vaccine.

• Tuberculosis and Respiratory Diseases
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• v.44 no.3
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• pp.534-546
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• 1997

Background : The p53 and retinoblastoma(Rb) tumor suppressor genes are associated with the pathogenesis of several types of human cancer. Substantial proportion of the primary lung cancers or cell lines have been reported to have the p53 and/or the Rb gene mutations. But, so far there is no report on the analysis of the Rb gene polymorphism as one of the genetic susceptibility marker. This study was undertaken to establish the gene frequencies of the polymorphic genotypes of the p53 and Rb genes in Koreans to evaluate the possible involvement of these genotypes as a risk factor of lung cancer. Methods : In this study 145 controls without previous and present tumor history and 128 lung cancer patients were subjected to analysis. The two intragenic polymorphisms of the p53 gene(exon 4/ AccII, intron 6/MspI) and one intron 17/XbaI polymorphism of the Rb gene were analysed by the method of polymersae chain reaction- restriction fragment length polymorphisms(PCR-RFLPs). The genotype of the intron 3/16 bp repeat polymorphism of p53 was determined by PCR and direct gel electrophoresis. Results : There were no significant differences in the genotype distributions of the p53 gene between lung cancer patients and controls. But heterozygotes(Arg/Pro) of the exon 4/AccII polymorphisms were slightly over-represented than controls, especially in the Kreyberg type I cancer, which was known to be associated with smoking. The intron 3/16 bp duplication and the intron 6/MspI polymorphisms were in complete linkage disequilibrium. About 95% of the individuals were homozygotes of the common alleles both in the 16 duplication and MspI polymorphisms, and no differences were deteced in the genotype distributions between lung cancer patients and controls. Overall genotype distributions of the Rb gene polymorphisms between lung cancer patients and controls were not significantly different However, the genotype distributions in the Kreyberg type I cancer were significantly different from those of controls(p = 0.0297) or adenocarcinomas(p = 0.0008). It was noticeable that 73.4% of the patients with adenocarcinomas were heterozygotes(r1/r2) whereas 39.2% of the Kreyberg type I cancer were heterozygous at this polymorphisms. In the lung cancer patients, significant differences were also noted between the high dose smokers and low dose smokers including non-smokers(p = 0.0258). The relative risk to Kreyberg type I cancer was significantly reduced in the individuals with the genotype of r1/r2(odds ratio = 0.46, 95% C.I. = 0.25-0.86, p = 0.0124). The combined genotype distribution of the exon 4 AccII of the p53 and the intron 17 Rb gene polymorphisms in Kreyberg type I cancers were significantly different from dose of controls or adenocarcinomas. The highest odds ratio were observed in the individuals with the genotypes of Arg/Pro and r2/r2(odds ratio = 1.97,95% C.I. = 0.84-4.59) and lowest one was in the patients with Arg/Arg, r1/r2 genotype(odds ratio = 0.54, 95% C.I. = 0.25-1.14). Conclusion : The p53 and the Rb gene polymorphisms modulate the risk of smoking induced lung cancer development in Koeans. However, the exact mechanism of risk modulation by these polymorphism remains to be determined. For more discrete clarification of associations between specific genotypes and lung cancer risk, the evaluations of these polymorphisms in other ethnics and more number of patients will be needed.

• Journal of Life Science
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• v.25 no.8
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• pp.861-869
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• 2015

One of the domesticated species; the dog has been selectively bred for various aims by human. The dog has many breeds, which are artificially selected for specific behaviors and morphologies. Dogs contribute their life to human as working dogs for guide, rescue, detection or etc. Working dogs requires good personality, such as gentleness, robustness and patience for performing their special duty. Many studies have concentrated on finding genetic marker for selecting the high-quality working dog. In this study, we confirmed quantitative expression patterns of eight genes (ABAT; 4-Aminobutyrate Aminotransferase, PLCB1; Phospholipase C, Beta 1, SLC10A4; Solute Carrier Family 10, Member 4, WNT1; Wingless-Type MMTV Integration Site Family, Member 1, BARX2; BarH-Like Homeobox 2, NEUROD6; Neuronal Differentiation 6, SEPT9; Septin 9 and TBR1; T-Box, Brain, 1) among brains tissues from four dog breeds (Beagle, Sapsaree, Shepherd and Jindo), because these genes were expressed and have functions in brain mostly. Specially, BARX2, SEPT9, SLC10A4, TBR1 and WNT1 genes were highly expressed in Beagle and Jindo, and Sapsaree and German Shepherd were vice versa. The biological significance of total genes was estimated by database for annotation, visualization and integrated discovery (DAVID) to determine a different gene ontology (GO) class. In these analyses, we suppose to these eight genes could provide influential information for brain development, and intelligence of organisms. Taken together, these results could provide clues to discover biomarker related to functional traits in brain, and beneficial for selecting superior working dogs.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.53-53
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• 2015

Agrobacterium tumefaciens-mediated transformation(ATMT) of Flammulina velutipes was used to produce a diverse number of transformants to discover the functions of gene that is vital for its variation color, spore pattern and cellulolytic activity. Futhermore, the transformant pool will be used as a good genetic resource for studying gene functions. Agrobacterium-mediated transformation was conducted in order to generate intentional mutants of F. velutipes strain KACC42777. Then Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into F. velutipes. This method is use to determine the functional gene of F. velutipes. Inverse PCR was used to insert T-DNA into the tagged chromosomal DNA segments and conducting sequence analysis of the F. velutipes. But this experiment had trouble in diverse morphological mutants because of dikaryotic nature of mushroom. It needed to make monokaryotic fruiting varients which introduced genes of compatible mating types. In this study, next generation sequencing data was generated from 28 strains of Flammulina velutipes with different phenotypes using Illumina Hiseq platform. Filtered short reads were initially aligned to the reference genome (KACC42780) to construct a SNP matrix. And then we built a phylogenetic tree based on the validated SNPs. The inferred tree represented that white- and brown- fruitbody forming strains were generally separated although three brown strains, 4103, 4028, and 4195, were grouped with white ones. This topological relationship was consistently reappeared even when we used randomly selected SNPs. Group I containing 4062, 4148, and 4195 strains and group II containing 4188, 4190, and 4194 strains formed early-divergent lineages with robust nodal supports, suggesting that they are independent groups from the members in main clades. To elucidate the distinction between white-fruitbody forming strains isolated from Korea and Japan, phylogenetic analysis was performed using their SNP data with group I members as outgroup. However, no significant genetic variation was noticed in this study. A total of 28 strains of Flammulina velutipes were analyzed to identify the genomic regions responsible for producing white-fruiting body. NGS data was yielded by using Illumina Hiseq platform. Short reads were filtered by quality score and read length were mapped on the reference genome (KACC42780). Between the white- and brown fruitbody forming strains. There is a high possibility that SNPs can be detected among the white strains as homozygous because white phenotype is recessive in F. velutipes. Thus, we constructed SNP matrix within 8 white strains. SNPs discovered between mono3 and mono19, the parental monokaryotic strains of 4210 strain (white), were excluded from the candidate. If the genotypes of SNPs detected between white and brown strains were identical with those in mono3 and mono19 strains, they were included in candidate as a priority. As a result, if more than 5 candidates SNPs were localized in single gene, we regarded as they are possibly related to the white color. In F. velutipes genome, chr01, chr04, chr07,chr11 regions were identified to be associated with white fruitbody forming. White and Brown Fruitbody strains can be used as an identification marker for F. veluipes. We can develop some molecular markers to identify colored strains and discriminate national white varieties against Japanese ones.

• Journal of Life Science
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• v.30 no.3
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• pp.313-319
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• 2020

Recently, cattle epidemic diseases are caused by a pathogen such as a virus or bacterium. Such diseases can spread through various pathways, such as feed intake, respiration, and contact between livestock. Diagnosis based on the ELISA (Enzyme-linked immunosorbent assay) and PCR (Polymerase chain reaction) methods has limitations because these traditional diagnostic methods are time consuming assays that require multiple steps and dedicated equipment. In this review, we propose the use of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas system based on DNA and RNA levels for early point-of-care diagnosis in cattle. In the CRISPR/Cas system, Cas effectors are classified into two classes and six subtypes. The Cas effectors included in class 2 are typically Cas9 in type II, Cas12 in type V (Cas12a and Cas12b) and Cas13 in type VI (Cas13a and Cas13b). The CRISPR/Cas system uses reporter molecules that are attached to the ssDNA strands. When the Cas enzyme cuts the ssDNA, these reporters either fluoresce or change color, indicating the presence of a specific disease marker. There are several steps in the development of a CRISPR/Cas system. The first is to select the Cas enzyme depending on DNA or RNA from pathogens (viruses or bacteria). Based on that, the next step is to integrate the optimal amplification, transducing method, and signal reporter. The CRISPR/Cas system is a powerful diagnostic tool using a gene-editing method, which is faster, better, and cheaper than traditional methods. This system could be used for early diagnosis of epidemic cattle diseases and help to control their spread.

• Korean Journal of Poultry Science
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• v.36 no.3
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• pp.207-213
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• 2009

Adenylosuccinate lyase (ADSL) deficiency is a disease of purine metabolism which affects patients both biochemicall and behaviorally. An obstacle of this purine nucleotide cycle(PNC) can be caused brain functional disorder and growth disorder. So ADSL deficiency, which is associated with sever mental retardation, autistic features and energy metabolism. This study was performed to identify SNP on ADSL gene in chicken. The nucleotides were observed as T to C ($7724^{th}$ nucleotide), C to T ($7732^{nd}$ nucleotide), G to T ($10108^{th}$ nucleotide), A to T ($10356^{th}$ nucleotide), G to A($10375^{th}$ nucleotide), A to C ($10402^{nd}$ nucleotide), A to T ($12716^{th}$ nucleotide), T to A ($12717^{th}$ nucleotide), C to T ($15491^{st}$ nucleotide), C to T ($15542^{nd}$ nucleotide) and C to T ($15550^{th}$ nucleotide). The nucleotide substitutions at $15542^{nd}$ and $15550^{th}$ (GeneBank accession no. AY665559) were found as missense mutation (alanine$\rightarrow$valine, proline$\rightarrow$serine, respectively). This study will be useful for farther researches for identifying association between these SNPs and energy metabolism in chicken. The C15550T SNP showed three genotypes, CC, CT, TT by digestion with the genotype TT had significantly faster the first lay day (150.0) than CT (162.0, P<0.05) and genotype TT (150.0, P<0.05) had significantly higher the egg production rate than CT (172.4, P<0.05). According to result of this study, a C15550T was found to have a significantly effect first lay day and mean egg production. It will be possible to use SNP marker on selecting chicken to improve important economic traits, which is the first lay day and mean egg production.

• Tuberculosis and Respiratory Diseases
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• v.47 no.2
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• pp.150-160
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• 1999

Background: The CREST syndrome is an indolent form of progressive systemic sclerosis. Although its clinical progress is indolent, pulmonary hypertension(PH) associated with CREST syndrome have grave prognosis with over 40 percent mortality rate at 2 year follow-up. But the pathogenesis of pulmonary hypertension in this disease is not known, and classified as either primary or secondary PH. Clonality of endothelial cell proliferation in plexiform lesion is a molecular marker which allows distinction between primary and secondary PH. We performed this study to know whether the PH associated with CREST syndrome is a variant of primary PH or is a secondary PH. Methods: We assessed the X-chromosome inactivation based on the methylation pattern of the human androgen-receptor gene by PCR(HUMARA). Endothelial cells in plexiform lesions from female patients(n=3) with PH associated with CREST syndrome were microdissected from paraffin blocks. Vascular smooth muscle cells and lung parenchyma were also microdissected for clonality studies. Results: The proliferating endothelial cells in 14 plexiform lesions were all polyclonal. Similarly proliferated smooth muscle cells from 5 vessels with medial hypertrophy were also polyclonal. Conclusion: These results suggest that the pulmonary hypertension associated with CREST syndrome has different pathogenesis from primary PH and to be classified as secondary PH.