• Tuberculosis and Respiratory Diseases
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• v.62 no.5
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• pp.406-416
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• 2007

Background: Single nucleotide polymorphisms (SNPs), which consist of a substitution of a single nucleotide pair, are the most abundant form of genetic variations occurring with a frequency of approximately 1 per 1000 base pairs. SNPs by themselves do not cause disease but can predispose humans to disease, modify the extent or severity of the disease or influence the drug response and treatment efficacy. Single nucleotide polymorphisms (SNPs), particularly those within the regulatory regions of the genes often influence the expression levels and can modify the disease. Studies examining the associations between SNP and the disease outcome have provided valuable insight into the disease etiology and potential therapeutic intervention. Traditionally, the genotyping of SNPs has been carried out using polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP), which is a low throughput technique not amenable for use in large-scale SNP studies. Recently, TaqMan real-time PCR chemistry was adapted for use in allelic discrimination assays. This study validated the accuracy and utility of real-time PCR technology for SNPs genotyping Methods: The SNPs in promoter sequence (-37 and -524) of lung cancer suppressor gene, RRM1 (ribonucleotide reductase M1 subunit) with the genomic DNA samples of 89 subjects were genotyped using both real-time PCR and PCR-RFLP. Results: The discordance rates were 2.2% (2 mismatches) in -37 and 16.3% (15 mismatches) in -524. Auto-direct sequencing of all the mismatched samples(17 cases) were in accord with the genotypes read by real-time PCR. In addition, 138 genomic DNAs were genotyped using real-time PCR in a duplicate manner (two separated assays). Ninety-eight percent of the samples showed concordance between the two assays. Conclusion: Real-time PCR allelic discrimination assays are amenable to high-throughput genotyping and overcome many of the problematic features associated with PCR-RFLP.

• Economic and Environmental Geology
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• v.17 no.2
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• pp.115-139
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• 1984

The Cu-Pb-Zn-Ag hydrothermal vein-type deposits which comprise the Sambong mine occur within calc-alkaline volcanics of the Cretaceous Gyeongsang Basin. The ore mineralization took place through three distinct stages of quartz (I and II stages) and calcite veins (III stage) which fill the pre-existing fault breccia zones. These stages were separated in time by tectonic fracturing and brecciation events. The reflection variations of one mineral depending on mineralization sequence are considered to be resulted from variation in its chemical composition due to different physico-chemical conditions in the hydrothermal system. The reflection power of sphalerite increases with the content of Fe substituted for Zn. Reflectances of the sphalerite grain are lower on (111) than on (100) surface. The spectral profiles depend on the internal reflection color. Sphalerite, showing green, yellow and reddish brown internal reflection, have the highest reflection power at $544m{\mu}$ (green), $593m{\mu}$ (yellow) and $615m{\mu}$ (red) wavelength, respectively. Chalcopyrite is recognized as biaxial negative from the reflectivity data of randomly oriented grains measured at the most sensitivity at $544m{\mu}$. The microindentation hardness against the Fe content (wt. %) for the sphalerite increases to 8.05% Fe and then decreases toward 9.5% Fe content. Vickers hardness of the sphalerite is considerably higher on surface of (100) than on (111). The relationship between Vickers hardness and crystal orientation of the galena was determined to be $VHN_{(111)}$ > $VHN_{(210)}$ > $VHN_{(100)}$. The softer sulfides have the wider variation of the diagonal length in the indentation. Diagonal length in the indentation is pyrite

• Journal of Life Science
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• v.32 no.12
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• pp.947-955
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• 2022

Silkworms, which have recently shown promise as functional health foods, show functional differences between varieties; therefore, the need for variety identification is emerging. In this study, we analyzed the whole silkworm genome to identify 10 unique silkworm varieties (Baekhwang, Baekok, Daebaek, Daebak, Daehwang, Goldensilk, Hansaeng, Joohwang, Kumkang, and Kumok) using single nucleotide polymorphisms (SNP) present in the genome as biomarkers. In addition, nine SNPs were selected to discriminate between varieties by selecting SNPs specific to each variety. We subsequently created a decision tree capable of cross-verifying each variety and classifying the varieties through sequential analysis. Restriction fragment length polymorphism (RFLP) was used for SNP867 and SNP9183 to differentiate between the varieties of Daehwang and Goldensilk and between Kumkang and Daebak, respectively. A tetra-primer amplification refractory (T-ARMS) mutation was used to analyze the remaining SNPs. As a result, we could isolate the same group or select an individual variety using the nine unique SNPs from SNP780 to SNP9183. Furthermore, nucleotide sequence analysis for the region confirmed that the alleles were identical. In conclusion, our results show that combining SNP analysis of the whole silkworm genome with the decision tree is of high value as a discriminative marker for classifying silkworm varieties.

• Journal of the Korean Wood Science and Technology
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• v.7 no.2
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• pp.3-30
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• 1979

Larch ($\underline{Larix}$ $\underline{leptolepis}$ GORDON), one of the major afforestation species in Korea in view of its growing stock and rate of growth, is not favored as a raw material for pulp due to its low yield of pulp and difficulties with bleaching arising from the high content of extractives in wood, and the high heartwood ratio and the active phenolics, respectively. The purpose of this study is to investigate the characteristics of firstly pulping with various additives of cellulose protector for the yield of pulp, and secondly bleaching with oxygen for chlotination-alkali extraction of five stage-sequence to reduce chlorine compounds in bleaching effluents. The kraft cooking liquor for five age groups of larchwood was 18 percent active alkali with 25 percent sulfidity and 5 : 1 liquor-to-wood ratio, and each soda liquor for sap-and heart-wood of the 15-year-old larchwood was 18 percent alkali having one of the following cellulose protectors as the additive; magnesium sulfate ($MgSO_4$, 2.5%), zinc sulfate ($ZnSO_4$, 2.5%), aluminium sulfate ($Al_2(SO_4)_3$, 2.5%), potasium iodide (KI, 2.5%), hydroquinone (HQ, 2.5%), anthraquinone (AQ, 0.1%) and ethylene diamine (EDA, 2.5%). Then each anthraquinone-soda liquor for the determination of suitable cooking condition was the active alkali level of 15, 17 and 19 percent with 1.0, 0.5 and 0.1 percent anthraquinone, respectively. The cooking procedure for the pulps was scheduled to heat to 170$^{\circ}C$ in 90 minutes and to cook 90 minutes at the maximum temperature. The anthraquinone-soda pulps from both heartwood and sapwood of 15-year-old larchwood prepared with 0.5 percent anthraquinone and 18 percent active alkali were bleached in a four-stage sequency of OCED. (O: oxygen bleaching, D: chlorine dioxide bleaching and E: alkali extraction). In the first stage oxygen in atmospheric pressure was applied to a 30 percent consistency of pulp with 0.1 percent magnesium oxide (MgO) and 3, 6, and 9 percent sodium hydroxide on oven dry base, and the bleached results were compared pulps bleached under the conventional CEDED (C: chlorination). The results in the study were summarized as follows: 1. The screened yield of larch kraft pulp did not differ from particular ages to age group, but heartwood ratio, basic density, fiber length and water-extractives contents of wood and the tear factor of the pulp increased with increasing the tree age. The total yield of the pulp decreased. 2. The yield of soda pulp with various chemicals for cellulose protection of the 15-year-old larchwood increased slightly more than that of pure soda pulp and was slightly lower than that of kraft pulp. The influence of cellulose protectors was similar to the yield of pulps from both sapwood and heartwood. The effective protectors among seven additives were KI, $MgSO_4$ and AQ, for which the yields of screened pulp was as high as that of kraft pulp. Considering the additive level of protector, the AQ was the most effective in improving the yield and the quality of pulp. 3. When the amount of AQ increased in soda cooking, the yield and the quality of the pulp increased but rejects in total yield increased with decreasing the amount of active alkali from 19 to 15 percent. The best proportion of the AQ seemed to be 0.5 percent at 17 percent active alkali in anthraquinone-soda pulping. 4. On the bleaching of the AQ-soda pulp at 30 percent consistency with oxygen of atomospheric pressure in the first stage of the ODED sequence, the more caustic soda added, the brighter bleached pulp was obtained, but more lignin-selective bleaching reagent in proportion to the oxygen was necessary to maintain the increased yield with the addition of anthraquinone. 5. In conclusion, the suitable pulping condition for larchwood to improve the yield and quality of the chemical pulp to the level for kraft pulp from conventional process seemed to be. A) the selection of young larchwood to prevent decreasing in yield and quality due to the accumulation extractives in old wood, B) the application of 0.5 percent anthraquinone to the conventional soda cooking of 18 percent active alkali, and followed, C) the bleaching of oxygen in atmospheric pressure on high consistency (30%) with 0.1 percent magnesium oxide in the first stage of the ODED sequence to reduce the content of chlorine compounds in effluent.

• 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 Korean Society of Forest Science
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• v.50 no.1
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• pp.56-71
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• 1980

To study the changes of vegetational composition of each plant successional stage of Pinus densiflora forest caused by pine gall midge damage, Thecodiplosis japonensis, located in Kyonggi-do area, the middle part of Korea, four districts, Anseong, Yongin, Gwangju, and Gapyeong, were selected according to the length of insect damage duration. The forest in the Anseong district was the noninfested one selected as the check. And forests in Yongin, Gwangju, and Gapyeong were the recent]y damaged, severely damaged, and damage prolonged ones in sequence. It was considered that this order could be in concord with the gradual transition of plant successional stage. In view of temperature, precipitation and soil factors, these four districts were sited within the same environment. Four survey plots were selected from each district and the distance between them was 3~4 km. Then again four subplots were set within a plot. Through needle accumulation after insect infestation, light intensity, soil moisture content, and the amount of soil organic matter were increased and these conditions could create a favorable environment enabling the new species invasion and their growth. These were naturally closely related with the increase in quantity of Pinus densiflora defoliation. After considerable time lapse, the quantities of above mentioned factors decreased with the development of the new substitute tree species. It was found that Quercus mongolica was an excellently substitute tree species come first in this studied area. Species diversity increased to a degree at the early stage of the duration of pine gall midge damage and decreased thereafter. As the same manner, similarity index value between plots in the same district decreased to a degree and increased thereafter. This was linked admittedly with the increase and decrease of tree species and evenness. Synthesizing above mentioned results, the process of plant succession studied quantitatively by changes of relative density and relative importance value, it can be concluded that Pinus densiflora forest gives way to Genus Quercus forest in which Genus Lespedeza and Genus Rhododendron species become as subdominance species after removal of the Pinus densiflora trees damaged by pine gall midge.

• Biomedical Science Letters
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• v.4 no.1
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• pp.11-25
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• 1998

The HLA genes located in the short arm of chromosome 6 specify heterodimeric glycoproteins involved in the regulation of the immune response. Recently, in the elucidation of HLA polymorphism, serological and cellular typing methods have been replaced by DNA typing using polymerase chain reaction (PCR). The purpose of this study was to establish the HLA DNA typing methods and determine gene frequencies of HLA molecules in Koreans. PCR-SSP (sequence specific primers) and PCR-RFLP (restriction fragment length polymorphism) techniques were used for the analysis of HLA-A, -B, -C, DRBl genes and HLA-DQAl, DQBl, DPBl genes, respectively. The results of B-lymphoblastoid cells used for control experiment were consistent with the previous data identified in the 11th International Histocompatibility Workshop. Seventeen, 23, 16, 8, 16, 13 and 37 types of HLA-A, B, C, DQAl, DQBl, DPBl and DRBl alleles were found, respectively, in a total of unrelated 120 Korean individuals. The most frequent HLA alleles were $A^*$02 (27.0%), B$^*$40 (17.6%), Cw$^*$01 (19.2%), DQAl$^*$0301 (32.1%), DQBl$^*$0303 (12.9%), DPBl$^*$0501 (31.3%) and DRBl$^*$1501 (9.2%) among Koreans. This study shows that DNA typing method using PCR technique is a relatively simple, fast and practical tool for the determination of the HLA-class I and II genes. Moreover, the data of HLA gene frequencies could be useful for the Korean database before clinical applications, including organ and unrelated bone marrow transplantation, anthropological study, disease association and individual identification.

• Research in Plant Disease
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• v.10 no.4
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• pp.241-247
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• 2004

Recently, we reported a satellite RNA (Paf-satRNA) which is encapsidated in a pepper isolate of Cucumber mosaic virus (CMV-Paf) regulated symptom attenuation of the helper virus. To characterize mild symptom domain of Paf-satRNA, a series of chimeric cDNAs of satRNAs were created by using full-length cDNA clones of Paf-satRNA and a Pep-satRNA, chlorosis-inducing satRNA in pepper plants, and analyzed for determinants of symptom attenuation. When compared the nucleotide sequences, the 3' and 5' terminal sequences of the two wild-type (wt) satRNAs contained relatively conserved sequences which are the typical to CMV satRNA. Ten bases insertions were found in PepY-satRNA, and two variable regions, 81st to 113th and 183rd to 265th from the 5'-end, were located in the middle parts of the satRNAs. To delineate the attenuated symptom-related domain for the Paf-satRNA, in vitro transcripts RNAs transcribed from the wt cDNAs and constructed chimeric cDNAs were combined with genomic RNAs, RNA1, RNA2 and RNA3, of CMV-Fny and inoculated onto Nicotiana benthamiana plants. These transcripts were fully infectious onto the N. benthamiana and infectivity was confirmed by the RT-PCR. Chimeric Paf(H/N)-satRNA and PepY(N/A)-satRNA as well as Paf-satRNA induced very mild mosaic or symptomless infection on N. benthamiana. By contrast, typical mosaic symptom and stunting of infected plants were induced when PepY-satRNA, PepY(H/N)-satRNA and Paf(N/A)-satRNA were infected to N. benthamiana. Paf-satRNA coinfected with CMV-Fny RNAs induced very mild to sympomless on pepper plants whereas PepY-satRNA-infected pepper expressed typical chlorosis mosaic symptom. Two kinds of chimeric mutants, Paf(H/N)-satRNA and PepY(N/A)-satRNA, induced mild mosaic or symptomless infection onto pepper plants, while PepY(H/N)-satRNA and Paf(N/A)-satRNA showed typical chlorosis and mosaic symptom with stunting. This results suggest that mild symptom-related domain for the Paf-satRNA was located on HpaI-NarI region.

• Tuberculosis and Respiratory Diseases
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• v.45 no.3
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• pp.529-535
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• 1998

Background: Interleukin-4 plays an important role in pathogenesis of asthma, especially in developing atopy by means of switching B lymphocytes to produce IgE. It has been shown that there is polymorphism in the Interleukin-4 promoter region, transversion of cytosine to thymine at-598 from translation initiation site of IL-4 gene. There has also been quite a few works to reveal the role of the polymorphism of IL-4 gene in patients with asthma. We performed this investigation to determine the role of the polymorphism in the severity of symptoms of patients with asthma. We also examined the frequency and the type of the polymorphism in asthmatics compared with non-asthmatics as well. Method: The subjects enrolled in this study were 49 asthmatics and 33 non-asthmatics. All the asthmatics were classified as mild and moderate to severe by the NHLBI/WHO Workshop. DNA from both asthmatics and non-asthmatics was extracted, then performed ARMS(Amplification Refractory Mutation System) as well as RFLP using BsmFl restriction enzyme in order to confirm the polymorphism of Il-4 gene. Results: There was no significant difference in the occurrence of polymorphism of the IL-4 promoter sequence between asthm and non-asthma groups(P=0.7). Among those with polymorphisms, the number of C/C type was slightly more than C/T type in both asthmatics and non-asthmatics, 26 vs 21 in asthmatics and 18 vs 15 in non-asthmatics, which was, however, insignificant statistically. No significant relationship between the severity of asthma and the polymorphism was found(P=0.7). Conclusion: There was no significant difference between the severity of asthma and the IL-4 promoter polymorphism(P=0.709). Interestingly, the frequency of the polymorphism in both asthmatics as well as non-asthmatics was found to be even higher than that occurred in Caucasians. However, no significant difference in the frequency of the polymorphism was found in both groups.

• Journal of the korean academy of Pediatric Dentistry
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• v.32 no.1
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• pp.75-88
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• 2005

Ameloblastoma is the most commonly occurring odontogenic tumor in oral cavity. Although most are benign epithelial neoplasm, they are generally considered to be locally aggressive and destructive, exhibiting a high rate of recurrence. The biological behavior of this neoplasm is a slowly growing, locally invasive tumor without metastasis, therefore malignant neoplasm, changed its histological appearance to carcinoma or showed distant metastasis, is only defined clinically. In this study, we identified the differentially expressed genes(DEGs) in stages under benign or malignant ameloblastoma compared with normal patient using ordered differential display(ODD) reverse transcription(RT)-PCR and $GeneFishing^{TM}$ technology. ODD RT-PCR is rather effective when the investigation of samples containing very small amounts of total RNA must be accomplished. ODD RT-PCR used the means of amplification with anchored T-primer and adaptor specific primer. bearing definite two bases at their 3' ends and so this method could display differential 3'-expressed sequence taqs(ESTs) patterns without using full-length cDNAs. Compared with standard differential display, ODD RT-PCR is more simple and have enough sensitivity to search for molecular markers by comparing gene expression profiles, However, this method required much effort and skill to perform. $GeneFishing^{TM}$ modified from DD-PCR is an improved method for detecting differentially expressed genes in two or more related samples. This two step RT-PCR method uses a constant reverse primer(anchor ACP-T) to prime the RT reaction and arbitrary primer pairs(annealing control primers, ACPs) during PCR. Because of high annealing specificity of ACPs than ODD RT-PCR, the application of $GeneFishing^{TM}$ to DEG discovery generates reproducible, authentic, and long(100bp to 2kb) PCR products that are detectable on agarose gels. Consequently, various DEGs observed differential expression levels on agarose gels were isolated from normal, benign, and malignant tissues using these methods. The expression patterns of the some isolated DEGs through ODD RT-PCR and $GeneFishing^{TM}$ were confirmed by Northern blot analysis and RT-PCR. The results showed that these identified DEGs were implicated in ameloblastoma neoplasm processes. Therefore, the identified DEGs will be further studied in order to be applied in candidate selection for marker as an early diagnosis during ameloblastoma neoplasm processes.