• Title/Summary/Keyword: Marker Technique

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Discrimination of Korean Soybean Cultivars by SSR Markers (SSR 마커에 의한 한국 콩 품종의 판별)

  • Kim, Seong-Hun;Chung, Jong-Wook;Moon, Jung-Kyung;Woo, Seon-Hee;Cho, Yong-Gu;Jong, Seung-Keun;Kim, Hong-Sig
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.51 no.7
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    • pp.658-668
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    • 2006
  • The objective of this study was to develop a technique for the cultivar discrimination using SSR markers in soybean. A total of 91 soybean cultivars developed from 1913 to 2002 in Korea were evaluated by five polymorphic SSR markers (Sat_043, Sat_036, Sat_022, Sat_088 and Satt045). Five SSR markers generated a total of 64 alleles and the number of alleles for each SSR marker ranged from 10 to 15 with average of 12.8. Polymorphic information contents (PIC) by five markers of 91 cultivars were ranged from 0.790 to 0.905 with average of 0.857. A total of 82 cultivars (90%) among 91 soybean cultivars could be individually discriminated by combination of five SSR markers through five step analysis. A cultivar, Buseok, by Sat_043 at the first step, 34 cultivars including Hojangkong by Sat_036 at the second step, 29 cultivars including Dankyeongkong by Sat_022 at the third step, 12 cultivars including Sinpaldalkong 2 by Sat_088 at the fourth step, and 6 cultivars including Saebyeolkong by Satt045 at the fifth step were discriminated. Soybean cultivars which were not discriminated by SSR markers could be discriminated by morphological characteristics.

Effects of GR89696 on parvalbumin positive neurons after cerebral ischemia in the Mongolian gerbil (몽고리안 저빌에서 뇌허혈시 GR89696이 parvalbumin 발현 신경세포에 미치는 영향)

  • Kwon, Young-bae;Yang, Il-suk;Lee, Jang-hern
    • Korean Journal of Veterinary Research
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    • v.39 no.1
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    • pp.34-44
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    • 1999
  • Ischemic damage in the selectively vulnerable populations of neurons is thought to be caused by an abnormal accumulation of intracellular calcium. It has been reported that the neurons, expressing specific calcium binding proteins, might effectively control intracellular calcium concentrations because of a high capacity to buffer intracellular calcium in the brain ischemic condition. It is uncertain that parvalbumin, one of the calcium binding proteins, can protect the neurons from the cerebral ischemic damage. Recently, treatment of kappa opioid agonists increased survival rate, improved neurological function, and decreased tissue damage under the cerebral ischemic condition. Many evidences indicate that these therapeutic effects might result from regulation of calcium concentration. This study was designed to analyze the changes of number in parvalbumin-positive neurons after cerebral ischemic damage according to timepoints after cerebral ischemic induction. In addition, we evaluated the effect of GR89696 (kappa opioid agonist) or naltrexone(non selective opioid antagonist) on the changes of number in parvalbumin expressing neurons under ischemic condition. Cerebral ischemia was induced by occluding the common carotid artery of experimental animals. The hippocampal areas were morphometrically analyzed at different time point after ischemic induction(1, 3, 5 days) by using immuno-histochemical technique and imaging analysis system. The number of parvalbumin-positive neurons in hippocampus was significantly reduced at 1 day after ischemia(p<0.05). Furthermore, the number of parvalbumin-immunoreactive neurons was dramatically reduced at 3 and 5 days after cerebral ischemic induction(p<0.05) as compared to 1 day group after ischemia, as well as sham control group. Significant reduction of parvalbumin positive neurons in CA1 region of hippocampus was observed at 1 day after cerebral ischemic induction. However, significant loss of MAP2 immunoreactivity was observed at 3 day after cerebral ischemia. The loss of parvalbumin-positive neurons and MAP2 immunoreactivity in CA1 region was prevented by pre-administration of GR89696 compared to that of saline-treated ischemic group. Furthermore, protective effect of GR89696 partially reversed by pre-treatment of naltrexone. These data indicate that parvalbumin-positive neurons more sensitively responded to cerebral ischemic damage than MAP2 protein. Moreover, this loss of parvalbumin-positive neurons was effectively prevented by the pretreatment of kappa opioid agonist. It was also suggested that the changes of number in parvalbumin-positive neurons could be used as the specific marker to analyze the degree of ischemic neuronal damage.

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Molecular Identification of Pooideae, Poaceae in Korea (국내 농경지에 발생하는 포아풀아과 잡초의 분자생물학적 동정)

  • Lee, Jeongran;Kim, Chang-Seok;Lee, In-Yong
    • Weed & Turfgrass Science
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    • v.4 no.1
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    • pp.18-25
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    • 2015
  • A universal DNA barcoding for agricultural noxious weeds is a powerful technique for species identification without morphological knowledge, by using short sections of DNA from a specific region of the genome. Two standard barcode markers, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used to examine the effectiveness of the markers for Pooideae barcoding using 163 individuals of 29 taxa across 16 genera of Korean Pooideae. The rbcL and ITS revealed a good level of amplification and sequencing success while matK did not. Barcode gaps were 78.6% for rbcL, 96.2% for matK, and 91.7% for ITS, respectively. Resolving powers were 89.3% for rbcL, 92.3% for matK, and 79.1% for ITS. The matK obtained the best both barcode gap and resolving power. However, it should be considered not to employ matK for Pooideae barcode because of low rate of PCR amplification and sequencing success. As a single DNA marker, rbcL and ITS were reasonable for Pooideae barcode. Barcode gap and resolving power were increased when ITS was incorporated into the rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use.

Bioactivity-guided isolation of ginsenosides from Korean Red Ginseng with cytotoxic activity against human lung adenocarcinoma cells

  • Yu, Jae Sik;Roh, Hyun-Soo;Baek, Kwan-Hyuck;Lee, Seul;Kim, Sil;So, Hae Min;Moon, Eunjung;Pang, Changhyun;Jang, Tae Su;Kim, Ki Hyun
    • Journal of Ginseng Research
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    • v.42 no.4
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    • pp.562-570
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    • 2018
  • Background: Lung cancer is the leading cause of cancer-related death worldwide. In this study, we used a bioactivity-guided isolation technique to identify constituents of Korean Red Ginseng (KRG) with antiproliferative activity against human lung adenocarcinoma cells. Methods: Bioactivity-guided fractionation and preparative/semipreparative HPLC purification were used with LC/MS analysis to separate the bioactive constituents. Cell viability and apoptosis in human lung cancer cell lines (A549, H1264, H1299, and Calu-6) after treatment with KRG extract fractions and constituents thereof were assessed using the water-soluble tetrazolium salt (WST-1) assay and terminal deoxyribonucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining, respectively. Caspase activation was assessed by detecting its surrogate marker, cleaved poly adenosine diphosphate (ADP-ribose) polymerase, using an immunoblot assay. The expression and subcellular localization of apoptosis-inducing factor were assessed using immunoblotting and immunofluorescence, respectively. Results and conclusion: Bioactivity-guided fractionation of the KRG extract revealed that its ethyl acetate-soluble fraction exerts significant cytotoxic activity against all human lung cancer cell lines tested by inducing apoptosis. Chemical investigation of the ethyl acetatesoluble fraction led to the isolation of six ginsenosides, including ginsenoside Rb1 (1), ginsenoside Rb2 (2), ginsenoside Rc (3), ginsenoside Rd (4), ginsenoside Rg1 (5), and ginsenoside Rg3 (6). Among the isolated ginsenosides, ginsenoside Rg3 exhibited the most cytotoxic activity against all human lung cancer cell lines examined, with $IC_{50}$ values ranging from $161.1{\mu}M$ to $264.6{\mu}M$. The cytotoxicity of ginsenoside Rg3 was found to be mediated by induction of apoptosis in a caspase-independent manner. These findings provide experimental evidence for a novel biological activity of ginsenoside Rg3 against human lung cancer cells.

No Effect of Diltiazem on the Hepatic Clearance of Indocyanine Green in the Rats

  • Joo, Eun-Hee;Lee, Yong-Bok
    • Archives of Pharmacal Research
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    • v.21 no.4
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    • pp.411-417
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    • 1998
  • In order to investigate the effect of the pretreatment with various doses of diltiazem (DTZ) on the pharmacokinetics of indocyanine green (ICG) at steady state, especially the hepatic blood clearance due to the change of hepatic blood flow, the following experiments were carried out with ICG, a hepatic function test marker, not metabolized in liver and only excreted in bile. The intravenous bolus injection ($3,780\mu\textrm{g}$/kg) and the constant-rate infusion ($10,100\mu\textrm{g}$/kg/hr) of ICG into the left femoral vein were made in order to check the steady-state plasma concentration ($C_{ss} of $10\mu\textrm{g}$/ml) of ICG at 20, 25 and 30 min. Following a 90-min washout period, the intravenous bolus injection (108, 430, 860 and $1,720\mu\textrm{g}$/kg) and the constant-rate infusion (108, 433, 866 and $1,730\mu\textrm{g}$/kg/hr) of DTZ into the right femoral vein were made and the achievement of the steady-state plasma levels ($C_{ss} of 50, 200, 400 and 800 ng/ml) of DTZ were conformed at 60, 70 and 80 min. During the steady state of DTZ, the intravenous bolus injection ($3,780\mu\textrm{g}$/kg) and the constant-rate infusion ($10,200\mu\textrm{g}$/kg/hr) of ICG into the left femoral vein were made and also the steady-state plasma concentration of ICG was checked at 20, 25 and 30 min. The plasma concentrations of DTZ and ICG were determined using a high performance liquid chromatographic technique. At the steady state, the hepatic blood clearance of ICG was obtained from the plasma concentration and blood-to-plasma concentration ratio ($R_B$) of ICG. The pretreatment with various doses of DTZ did not influence the plasma concentrations, $R_B$ and plasma free fraction ($f_p$) of ICG. So the hepatic blood clearance of ICG was independent of concentration of DTZ. The hepatic blood clearance of ICG could be affected by both hepatic bood flow and hepatic intrinsic clearance. But there was no change of the hepatic blood clearance of ICG between the control and the DTZ-pretreated rats in this study. So it may be suggested that DTZ does not influence hepatic blood flow.

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Human Immunodeficiency Virus-l Tat Positively Regulates the Human CD99 Gene via DNA Demethylation (Human Immunodeficiency Virus-1 Tat 단백에 의한 인간 CD99유전자의 조절기전에 대한 연구)

  • Lee, Eu-Gene;Kim, Ye-Ri;Lee, Mi-Kyung;Lee, Im-Soon
    • Korean Journal of Microbiology
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    • v.44 no.4
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    • pp.277-281
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    • 2008
  • HIV affects many organ systems. Patients with HIV infection have substantially increased risk of developing various cancers, primarily by opportunistic infection with oncogenic viruses due to their immunocompromised status. However, extensive evidence also indicates that the viral protein, Tat itself, may playas a major factor in the development of AIDS-related neoplasms. The molecular mechanism underlying Tat's oncogenic activity may include deregulation of cellular genes. Therefore, in this study, we examined the effect of HIV-l Tat on CD99 as one of the target cellular genes, which is a well-known tumor marker in several cancers. By using established HeLa clones that are stably expressing Tat, we found that CD99 is upregulated by endogenous Tat, whereas STAT3 is down regulated. Upon the screening of genes differentially expressed between Tat-stable cells and the control cells by using the gene fishing technique, DEG, we detected 3 genes which expression is affected by the presence of Tat. Furthermore, the methylation specific PCR analysis of the stably Tat expressing cell lines revealed that the CD99 promoter is de methylated in the presence of Tat. Taken together, these results open a potential role of CD99 in AIDS-related oncogenesis via epigenetic regulation by HIV-1 Tat.

Development of Molecular Detection Marks Using PCR-RFLP Technique for Arkshell (Scapharca broughtonii Schrenck) (피조개, Scapharca broughtonii Schrenck RFLP 마커 개발)

  • Cho Eun Seob;lung Choon Coo;Kim Chul Won;Sohn Sang Cyu
    • Journal of Life Science
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    • v.15 no.6 s.73
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    • pp.879-883
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    • 2005
  • This study was differentiated between Korea and China arkshells using PCR-aided RFLP method which could identify the variation for inter-and intra-species of arkshell (Scapharca broughtonii Schrenck) at the level of DNA. The DNA fragment patterns were compared after digesting gene of mitochondrial 16S rDNA with 8 kinds of restriction enzymes. A 720 bp DNA fragment corresponding to 16S rDNA gene was amplified by PCR with primers ArkF-3 and ArkR-3. PCR products were cut by restriction enzymes (Pvull, BamHI, Hinfl, HaeIII, EcoRI, RsaI, Ksp221, and BstX21), and RFLP pattern was studied. A unique 275 bp DNA band was observed in the samples from Dukyang, Gamak, Namhae, Jinhae, and Taean in Korea when treated by Hinfl, but Chinese arkshell did not show. Treatment of HaeIII could discriminate the sample of Namhae and Jinhae from Dukyang/Gamak/Taean, as well as Korean and Chinese arkshell based on a 700 bp. However, PuvII, BamHI, EcoRI, RsaI, Ksp221, and BstX21 showed the same of 700 bp band in Korean and Chinese arkshell. The phylogenetic tree inferred from PCR-RFLP pattern comparsion in Korean arkshell was different that the distance between Dukyang/Gamak/Taean and Namhae/Jinhae was approximately 7. In particular, the distance between Korean and Chinese arkshell was 25. Consequently, HinfI and HaeIII played an important role in a reliable molecular tool for rapid discriminating Korean and Chinese arkshell, as well as a intra-species in Korea.

Relationship between exhaled nitric oxide and pulmonary function test in children with asthma (소아 천식에서 호기산화질소와 폐기능 검사의 관계)

  • Ko, Han-Seok;Chung, Sung-Hoon;Choi, Yong-Sung;Choi, Sun-Hee;Rha, Yeong-Ho
    • Clinical and Experimental Pediatrics
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    • v.51 no.2
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    • pp.181-187
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    • 2008
  • Purpose : Asthma is characterized by reversible airway obstruction and bronchial hyperresponsiveness result from airway inflammation. Fraction of nitric oxide in expired air (FeNO) has recently been investigated as a noninvasive measure of airway inflammation. FeNO has been reported to correlate with induced sputum eosinophilia and methacholine challenge test that it is represent severity of asthma. The purpose of this study was to analyze the relationship of FeNO with pulmonary function tests in patients with intermittent asthma. Methods : Eighty children included in this study were diagnosed as asthma from April through August, 2005 in Department of Pediatrics, College of Medicine, Kyunghee University. They aged from 4 to 15 years who were able to conduct spirometry and FeNO monitoring. They did not have upper respiratory tract infection and did not use an asthma controller which contain corticosteroids within 4 weeks. Pulmonary function test was done and FeNO was measured with online tidal breathing method using a chemiluminescence NO analyzer (CLD 88 sp, Eco Medics, Duernten, Switzerland). The correlations between pulmonary function test and FeNO were analyzed using Spearman correlation coefficient method. Results : The mean of FeNO of subject was 16.88 parts per billion (ppb). The mean of forced expiratory volume in 1 second ($FEV_1$) was $0.890{\pm}0.455L$ and forced vital capacity (FVC) was $1.071{\pm}0.630L$. The mean of predicted $FEV_1%$ ($FEV_1%pred$) was $98.39{\pm}34.27%$ and $FEV_1/FVC$ was $88.53{\pm}19.49$. FeNO was significantly correlate with $FEV_1$ (r=0.345, P<0.01) and FVC (r=0.244, P<0.05). FeNO did not correlate with $FEV_1%pred$ or $FEV_1/FVC$. Conclusion : The measurement of FeNO could be a useful marker in the management of childhood asthma and it is evolving to provide a complementary role alongside existing pulmonary function test. We propose that measuring technique and establishment of normal reference range are important area for future research.

Studies of Molecular Breeding Technique Using Genome Information on Edible Mushrooms

  • Kong, Won-Sik;Woo, Sung-I;Jang, Kab-Yeul;Shin, Pyung-Gyun;Oh, Youn-Lee;Kim, Eun-sun;Oh, Min-Jee;Park, Young-Jin;Lee, Chang-Soo;Kim, Jong-Guk
    • 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.

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The Role of Lymphocyte Compartment and Cytokine in Coal Workers Pneumoconiosis (진폐증환자에서의 임파구 분획 및 싸이토카인의 역할)

  • Lee, Jung-Yeon;Yoo, Kwang-Ha;Ahn, Hae-Ryon;Kim, Sung-Ryul;Lee, Hae-Woon;Ahn, Cheol-Min;Kim, Hyung-Joong
    • Tuberculosis and Respiratory Diseases
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    • v.52 no.3
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    • pp.241-250
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    • 2002
  • Background : Coal-worker's pneumoconiosis(CWP) is characterized by a chronic inflammatory lung reaction associated with macrophage accumulation in the alveolar spaces. CWP is usually divided into two stage : simple pneumoconiosis(SP) where there are a limited number of fibrotic lesions remain limited, with radiological opacities smaller than 1cm and progressive massive fibrosis(PMF), which is characterized by the development of a perifocal extensive fibrotic response of the lung and severe alterations in pulmonary function. In this study, the lymphocyte compartment and cytokine were evaluated by measuring the serum levels in the control, SP and PMF groups. Materials and Methods : The coal workers selected for this study were employees(patients?) of the Tae-Baek and Dong-Hae hospital. All were men, 45-76 years old and the mean duration of their exposure to coal dust was 23.2 years in the lymphocyte compartment and 24.3 years in the cytokine checked group. According to X-ray examination results, the patients were classified into either one of the SP, PMF categories. The normal controls examined were 26-70 years old men. The serum cytokine levels were estimated by using an end point enzyme immunoassay technique. Results : T lymphocyte, helper and suppressor T cells were highly related to pneumoconiosis in this study. A statistically significant decrease in the number of suppressor T lymphocytes was observed in the simple pneumoconiosis patients and at the same time, there was an increase in the lymphocyte index. Howevere, there was no statistically difference in the serum cytokines levels among the SP, PMF and control groups. Conclusion : T lymphocyte, helper T, and suppressor T cells may be highly related to the development of CWP compared to the control group particularly in the early stage of pneumoconiosis. The changes observed in the immunological system in patients with pneumoconiosis may lie at the bottom of the pathogenesis of fibrosis. Further study is needed to evaluate the lymphocyte compartment as a marker for pneumoconiosis development in the early stage.