• Title/Summary/Keyword: Genome Analysis

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Evaluation of Germplasm and Development of SSR Markers for Marker-assisted Backcross in Tomato (분자마커 이용 여교잡 육종을 위한 토마토 유전자원 평가 및 SSR 마커 개발)

  • Hwang, Ji-Hyun;Kim, Hyuk-Jun;Chae, Young;Choi, Hak-Soon;Kim, Myung-Kwon;Park, Young-Hoon
    • Horticultural Science & Technology
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    • v.30 no.5
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    • pp.557-567
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    • 2012
  • This study was conducted to achieve basal information for the development of tomato cultivars with disease resistances through marker-assisted backcross (MAB). Ten inbred lines with TYLCV, late blight, bacterial wilt, or powdery mildew resistance and four adapted inbred lines with superior horticultural traits were collected, which can be useful as the donor parents and recurrent parents in MAB, respectively. Inbred lines collected were evaluated by molecular markers and bioassay for confirming their disease resistances. To develop DNA markers for selecting recurrent parent genome (background selection) in MAB, a total of 108 simple sequence repeat (SSR) primer sets (nine per chromosome at average) were selected from the tomato reference genetic maps posted on SOL Genomics Network. Genetic similarity and relationships among the inbred lines were assessed using a total of 303 polymorphic SSR markers. Similarity coefficient ranged from 0.33 to 0.80; the highest similarity coefficient (0.80) was found between bacterial wilt-resistant donor lines '10BA333' and '10BA424', and the lowest (0.33) between a late blight resistant-wild species L3708 (S. pimpinelliforium L.) and '10BA424'. UPGMA analysis grouped the inbred lines into three clusters based on the similarity coefficient 0.58. Most of the donor lines of the same resistance were closely related, indicating the possibility that these lines were developed using a common resistance source. Parent combinations (donor parent ${\times}$ recurrent parent) showing appropriate levels of genetic distance and SSR marker polymorphism for MAB were selected based on the dendrogram. These combinations included 'TYR1' ${\times}$ 'RPL1' for TYLCV, '10BA333' or '10BA424' ${\times}$ 'RPL2' for bacterial wilt, and 'KNU12' ${\times}$ 'AV107-4' or 'RPL2' for powdery mildew. For late blight, the wild species resistant line 'L3708' was distantly related to all recurrent parental lines, and a suitable parent combination for MAB was 'L3708' ${\times}$ 'AV107-4', which showed a similarity coefficient of 0.41 and 45 polymorphic SSR markers.

First Report of Soybean Dwarf Virus on Soybean(Glycine max) in Korea (콩(Glycine max)에서 콩위축바이러스(Soybean dwarf virus)의 최초 발생보고)

  • Kim, Sang-Mok;Lee, Jae-Bong;Lee, Yeong-Hoon;Choi, Se-Hoon;Choi, Hong-Soo;Park, Jin-Woo;Lee, Jun-Seong;Lee, Gwan-Seok;Moon, Jung-Kyung;Moon, Jae-Sun;Lee, Key-Woon;Lee, Su-Heon
    • Research in Plant Disease
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    • v.12 no.3
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    • pp.213-220
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    • 2006
  • In year 2003, a soybean(Glycine max) sample showing severe dwarfing symptom was collected from a farmers' field in Cheongsong in Korea. The results from the diagnosis of the sample by RT-PCR revealed that it was infected by Soybean dwarf virus(SbDV), SbDV-L81. This study could be the first report of the occurrence of the virus in Korea. To further characterize the virus, the partial nucleotide sequence of the genomic RNA of SbDV-L81 was determined by RT-PCR using species-specific primers. The sequences were analyzed and subsequently compared to previously characterized strains of SbDV based on the pattern of symptom expression and vector specificities. The intergenic region between ORF 2 and 3 and the coding regions of ORF 2, 3 and 4 were relatively similar to those of dwarfing strains(SbDV-DS and DP) rather than those of yellowing strains(SbDV-YS and YP). Likewise, the result from the analysis of 5'-half of the coding region of ORF5 indicated that SbDV-L81 was closely related to strains(SbDV-YP and DP) transmitted by Acyrthosiphon pisum. These data from the natural symptom and the comparisons of five regions of nucleotide sequences of SbDV suggested that SbDV-L81 might be closely related SbDV-DP.

Recombination and Expression of VP1 Gene of Infectious Pancreatic Necrosis Virus DRT Strain in a Baculovirus, Hyphantria cunea Nuclear Polyhedrosis Virus (전염성 췌장괴저바이러스 DRT Strain VP1유전자의 Baculovirus Hyphantria cunea Nuclear Polyhedrosis Virus에 재조합과 발현)

  • Lee, Hyung-Hoan;Chang, Jae-Hyeok;Chung, Hye-Kyung;Cha, Sung-Chul
    • The Journal of Korean Society of Virology
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    • v.27 no.2
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    • pp.239-255
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    • 1997
  • Expression of the cDNA of the VP1 gene on the genome RNA B segment of infectious pancreatic necrosis virus (IPNV) DRT strain in E. coli and a recombinant baculovirus were carried out. The VP1 gene in the pMal-pol clone (Lee et al. 1995) was cleaved with XbaI and transferred into baculovirus transfer vector, pBacPAK9 and it was named pBacVP1 clone. The VP1 gene in the pBacVP1 clone was double-digested with SacI and PstI and then inserted just behind T5 phage promoter and the $6{\times}His$ region of the pQE-3D expression vector, and it was called pQEVPl. Again, the $6{\times}$His-tagged VP1 DNA fragment in the pQEVP1 was cleaved with EcoRI and transferred into the VP1 site of the pBacVP1, resulting pBacHis-VP1 recombinant. The pBacHis-VP1 DNA was cotransfected with LacZ-Hyphantria cunea nuclear polyhedrosis virus (LacZ-HcNPV) DNA digested with Bsu361 onto S. frugiperda cells to make a recombinant virus. One VP1-gene inserted recombinant virus was selected by plaque assay. The recombinant virus was named VP1-HcNPV-1. The $6{\times}$His-tagged VP1 protein produced by the pQEVP1 was purified with Ni-NTA resin chromatography and analyzed by SDS-PAGE and Western blot analysis. The molecular weight of the VP1 protein was 94 kDa. The recombinant virus, VP1-HcNPV-1 did not form polyhedral inclusion bodies and expressed VP1 protein with 95 kDa in the infected S. frugiperda cells, which was detected by Western blot. The titer of the VP1-HcNPV-1 in the first infected cells was $2.0{\times}10^5\;pfu/ml$ at 7 days postinfection.

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Alcohol Fermentation at High Temperature and the Strain-specific Characteristics Required to Endow the Thermotolerance of Sacchromyces cerevisiae KNU5377

  • Paik, Sang-Kyoo;Park, In-Su;Kim, Il-Sup;Kang, Kyung-Hee;Yu, Choon-Bal;Rhee, In-Koo;Jin, In-Gnyol
    • Proceedings of the Korean Society for Applied Microbiology Conference
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    • 2005.06a
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    • pp.154-164
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    • 2005
  • Saccharomyces cerevisiae KNU5377 is a thermotolerant strain, which can ferment ethanol from wasted papers and starch at 40$^{\circ}C$ with the almost same rate as at 30$^{\circ}C$. This strain showed alcohol fermentation ability to convert wasted papers 200 g (w/v) to ethanol 8.4% (v/v) at 40$^{\circ}C$, meaning that 8.4% ethanol is acceptable enough to ferment in the industrial economy. As well, all kinds of starch that are using in the industry were converted into ethanol at 40$^{\circ}C$ with the almost same rate as at 30$^{\circ}C$. Hyperthermic cell killing kinetics and differential scanning calorimetry (DSC) revealed that exponentially growing cells of this yeast strain KNU5377 were more thermotolerant than those of S. cerevisiae ATCC24858 used as a control. This intrinsic thermotolernace did not result from the stability of entire cellular components but possibly from that of a particular target. Heat shock induced similar results in whole cell DSC profiles of both strains and the accumulation of trehalose in the cells of both strains, but the trehalose contents in the strain KNU5377 were 2.6 fold higher than that in the control strain. On the contrary to the trehalose level, the neutral trehalase activity in the KNU5377 cells was not changed after the heat shock. This result made a conclusion that though the trehalose may stabilize cellular components, the surplus of trehalose in KNU5377 strain was not essential for stabilization of whole cellular components. A constitutively thermotolerant yeast, S. cerevisiae KNU5377, was compared with a relatively thermosensitive control, S. cerevisiae ATCC24858, by assaying the fluidity and proton ATPase on the plasma membrane. Anisotropic values (r) of both strains were slightly increased by elevating the incubation temperatures from 25$^{\circ}C$ to 37$^{\circ}C$ when they were aerobically cultured for 12 hours in the YPD media, implying the membrane fluidity was decreased. While the temperature was elevated up to 40$^{\circ}C$, the fluidity was not changed in the KNU5377 cell, but rather increased in the control. This result implies that the plasma membrane of the KNU5377 cell can be characterized into the more stabilized state than control. Besides, heat shock decreased the fluidity in the control strain, but not in the KNU5377 strain. This means also there's a stabilization of the plasma membrane in the KNU5377 cell. Furthermore, the proton ATPase assay indicated the KNU5377 cell kept a relatively more stabilized glucose metabolism at high temperature than the control cell. Therefore, the results were concluded that the stabilization of plasma membrane and growth at high temperature for the KNU5377 cell. Genome wide transcription analysis showed that the heat shock responses were very complex and combinatory in the KNU5377 cell. Induced by the heat shock, a number of genes were related with the ubiquitin mediated proteolysis, metallothionein (prevent ROS production from copper), hsp27 (88-fold induced remarkably, preventing the protein aggregation and denaturation), oxidative stress response (to remove the hydrogen peroxide), and etc.

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Intake of Antioxidant Nutrients and Risk of Metabolic Syndrome according to Degree of Stress in Rural Korean Women (한국 농촌 여성의 스트레스 정도에 따른 항산화 영양소 섭취와 대사증후군 위험도)

  • Yoon, Jungwon;Shin, Yoonjin;Kang, Bori;Byeon, Suji;Kim, Soo A;Kim, Yangha
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.46 no.7
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    • pp.868-875
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    • 2017
  • The aim of the present study was to investigate antioxidant nutrient intake and risk of metabolic syndrome based on stress level in rural Korean women. Subject were participants from the Multi-Rural Communities Cohort Study, which was a part of the Korean Genome and Epidemiology Study. According to scores of the Psychosocial Well-Being Index Short-Form, a total of 10,111 subjects were classified into 'low stress group (n=8,015)' from 0 to 26 points and 'high stress group (n=2,096)' above 27 points. Data were collected using self-administered questionnaires, anthropometric measurements, and blood chemical analysis. Dietary nutrient consumption was assessed by a semi-quantitative food frequency questionnaire. High stress group showed lower intake of antioxidant nutrients, such as vitamin A, vitamin C, vitamin E, folate, zinc, and carotene compared to the low stress group. Intake of fruits and vegetable was lower in the high stress group compared to the low stress group. Subjects with high stress showed higher risk of hypertension [odd ratio (OR), 95% confidence interval (CI)=1.226 (1.112~1.351)] and hypertriglyceridemia [OR, 95% CI=1.227 (1.110~1.356)] than subjects with low stress. High stress group had a significantly greater odds ratio for metabolic syndrome compared with the low stress group [OR, 95% CI=1.216 (1.101~1.342]). Thus, the present study suggests that high stress might be associated with low intake of antioxidant nutrients and high risk of metabolic syndrome in rural Korean women.

Present status and prospect for development of mushrooms in Korea

  • Jang, Kab-Yeul;Oh, Youn-Lee;Oh, Minji;Im, Ji-Hoon;Lee, Seul-Ki;Kong, Won-Sik
    • 한국균학회소식:학술대회논문집
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    • 2018.05a
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    • pp.27-27
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    • 2018
  • The production scale of mushroom cultivation in Korea is approximately 600 billion won, which is 1.6% of the Korean gross agricultural output. Annually, ca. 190,000 tons of mushrooms are harvested in Korea. Although the numbers of mushroom farms and cultivators are constantly decreasing, the total mushroom yields are increasing due to the large-scale cultivation facilities and automation. The recent expansion of the well-being trend causes increase in mushroom consumption in Korea: annual per capita consumption of mushroom was 3.9kg ('13) that is a little higher than European's average. Thus the exports of mushrooms, mainly Flammulina velutipes and Pleurotus ostreatus, have been increased since the middle of 2000s. Recently, however, it is slightly reduced. However, Vietnam, Hong Kong, the United States, the Netherlands and continued to export, and the country has increased recently been exported to Australia, Canada, Southeast Asia and so on. Canned foods of Agaricus bisporus was the first exports of the Korean mushroom industry. This business has reached the peak of the sale in 1977-1978. As Korea initiated trade with China in 1980, the international prices of mushrooms were sharply fall that led to shrink the domestic markets. According to the high demand to develop new items to substitute for A. bisporus, oyster mushroom (Pleurotus ostreatus) was received the attention since it seems to suit the taste of Korean consumers. Although log cultivation technique was developed in the early 1970s for oyster mushroom, this method requires a great deal of labor. Thus we developed shelf cultivation technique which is easier to manage and allows the mass production. In this technique, the growing shelf is manly made from fermented rice straw, that is the unique P. ostreatus medium in the world, was used only in South Korea. After then, the use of cotton wastes as an additional material of medium, the productivity. Currently it is developing a standard cultivation techniques and environmental control system that can stably produce mushrooms throughout the year. The increase of oyster mushroom production may activate the domestic market and contribute to the industrial development. In addition, oyster mushroom production technology has a role in forming the basis of the development of bottle cultivation. Developed mushroom cultivation technology using bottles made possible the mass production. In particular, bottle cultivation method using a liquid spawn can be an opportunity to export the F.velutipes and P.eryngii. In addition, the white varieties of F.velutipes were second developed in the world after Japan. We also developed the new A.bisporus cultivar "Sae-ah" that is easy to grown in Korea. To lead the mushroom industry, we will continue to develop the cultivars with an international competitive power and to improve the cultivation techniques. Mushroom research in Korea nowadays focuses on analysis of mushroom genetics in combination with development of new mushroom varieties, mushroom physiology and cultivation. Further studied are environmental factors for cultivation, disease control, development and utilization of mushroom substrate resources, post-harvest management and improvement of marketable traits. Finally, the RDA manages the collection, classification, identification and preservation of mushroom resources. To keep up with the increasing application of biotechnology in agricultural research the genome project of various mushrooms and the draft of the genetic map has just been completed. A broad range of future studies based on this project is anticipated. The mushroom industry in Korea continually grows and its productivity rapidly increases through the development of new mushrooms cultivars and automated plastic bottle cultivation. Consumption of medicinal mushrooms like Ganoderma lucidum and Phellinus linteus is also increasing strongly. Recently, business of edible and medicinal mushrooms was suffering under over-production and problems in distribution. Fortunately, expansion of the mushroom export helped ease the negative effects for the mushroom industry.

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Effect of Carthami Tinctorii Fructus Herbal-acupuncture Solution(CTF-HAS) on Gene Expression in HepG2 carcinomar cells (Oligonucleotide chip를 이용한 홍화자약침액(紅花子藥鍼液)이 간암세포주(肝癌細胞柱)의 유전자(遺傳子) 발현(發顯)에 미치는 영향(影響))

  • Lee, Kyung-min;Lim, Seong-chul;Jung, Tae-young;Seo, Jung-chul;Han, Sang-won
    • Journal of Acupuncture Research
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    • v.22 no.3
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    • pp.215-225
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    • 2005
  • Objective : It has long been known about the osteogenic effect of CTF-HAS on bone tissues. However, it has not been determined the effect of CTF-HAS on cancer cells. The purpose of this study is to screen the CTF-HAS mediated differentially expressed genes in cancer cells such as HepG2 hepatoma cells lines. Oligonucleotide microarray approach were employed to screen the differential expression genes. Methods : CTF-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of CTF-HAS(0.1, 0.5, 1.5, 10, $20mg/m{\ell}$) for 24 h. Cytotoxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with $1.5mg/m{\ell}$ of CTF-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide genechip (Human genome U133 Plus 2.0., Affimatrix Co.). ResuIts : It has no cytotoxic effects on HepG2 cells in all concentrations (0.1, 0.5, 1.5, 10, $20mg/m{\ell}$). More than twofold up-regulated genes were 19 genes. The number of more than twofold down-regulated genes was 13. Discussion : This study showed the screening of CTF-HAS mediated differentially regulated genes using combined approaches of oligonucleotide microarray. The screened genes will be used for the better understanding in therapeutic effect of CTF-HAS on cancer field.

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Assessment of the Specificity of A Hybridization of Surfactant Protein A by Addition of Non-specific Rat Spleen RNA (Surfactant Protein A mRNA을 이용한 유전자 재결합 반응에서 비특이성 RNA의 첨가에 의한 특이성 검정)

  • Kim, Byeong Cheol;Kim, Mi Ok;Kim, Tae-Hyung;Sohn, Jang Won;Yoon, Ho Joo;Shin, Dong Ho;Park, Sung Soo
    • Tuberculosis and Respiratory Diseases
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    • v.56 no.4
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    • pp.393-404
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    • 2004
  • Background : Nucleic acid hybridization has become an essential technique in the development of our understanding of gene structure and function. The quantitative analysis of hybridization has been used in the measurement of genome complexity and gene copy number. The filter hybridization assay is rapid, sensitive and can be used to measure RNAs complementary to any cloned DNA sequence. Methods : The authors assessed the accuracy, linearity, correlation coefficient and specificity of the hybridization depending on the added dose(0, 1, 5, and $10{\mu}g$) of non-specific rat spleen RNA to hybridization of surfactant protein A mRNA. Filter hybridization assays were used to obtain the equation of standard curve and thereby to quantitate the mRNA quantitation. Results : 1. Standard curve equation of filter hybridization assay between counts per minute (X) and spleen RNA input (Y) was Y=0.13X-19.35. Correlation coefficient was 0.98. 2. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) was Y=0.00066X-0.046. Correlation coefficient was 0.99. 3. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $1{\mu}g$ spleen RNA was Y=0.00056X-0.051. Correlation coefficient was 0.99. 4. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $5{\mu}g$ spleen RNA was Y=0.00065X-0.088. Correlation coefficient was 0.99. 5. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $10{\mu}g$ spleen RNA was Y=0.00051X-0.10. Correlation coefficient was 0.99. Conclusions : Comparison of cpm/filter in a linear range allowed accurate and reproducible estimation of surfactant protein A mRNA copy number irrespective of the addition dosage of non-specific rat spleen RNA over the range $0-10{\mu}g$.

Ser326Cys Polymorphism of hOGG1 Gene and Risk of Primary Lung Cancer in Koreans (한국인에서 hOGG1 유전자의 Ser326Cys 다형성과 원발성 폐암의 위험도)

  • Chae, Sang-Chul;Kim, Kyung-Rock;Joo, So-Young;Lee, Su-Yean;Kang, Kyung-Hee;Jeon, Kyung-Neoyh;Cha, Seung-Ick;Kim, Chang-Ho;Jung, Tae-Hoon;Park, Jae-Yang
    • Tuberculosis and Respiratory Diseases
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    • v.52 no.1
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    • pp.5-13
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    • 2002
  • Background: DNA repair plays a crucial role in protecting the genome from cancer-causing agents. Therefore, a reduced DNA repair capacity can increase the susceptibility to cancer. The human OGG1 (hOGG1) gene encodes DNA glycosylase/apurinic lyase and excise 8-hydroxyguanine, one of the major premutagenic DNA lesions, which is produced by oxygen radical forming agents including smoking. Recently several polymorphisms in the hOGG1 gene were identified, and it is possible that these polymorphism') may affect the DNA repair capacity and thus modulate cancer susceptibility. The relationship between the codon 326 polymorphism (Ser to Cys) in the hOGG1 gene and lung cancer risk was investigated. Materials and Method: The Ser326Cys genotypes were determined using PCR-RFLP analysis in 299 primary lung cancer patients and 186 healthy controls who were frequency (case:control=3:2) matched according to age and sex. Result: The frequencies of the Ser326Cys genotypes (Ser/Ser, Ser/Cys and Cys/Cys) among cases (23.4%, 51.8%, and 24.7%, respectively) were not significantly different from those among the controls (22.6%,52.1% and 25.3%, respectively). When the analyses were stratified according to age, sex, smoking status and packyears of smoking, no significant association between this polymorphism and lung cancer risk was found. Moreover, the Ser326Cys genotype showed no apparent relationship with any of the histological types of lung cancer. Conclusion: These result suggest that the hOGG1 Ser326Cys polymorphism is not a major contributor to individual lung cancer susceptibility in Koreans.

Microsatellite Alterations of Plasma DNA in Non Small Cell Lung Cancer (비소세포폐암 환자의 혈장 DNA를 이용한 Microsatellite 분석)

  • Kim, Kyu-Sik;Kim, Eun-Jung;Kim, Soo-Ock;Oh, In-Jae;Park, Chang-Min;Jeong, Ju-Yeon;Kim, Yu-Il;Lim, Sung-Chul;Park, Jong-Tae;Kim, Young-Chul
    • Tuberculosis and Respiratory Diseases
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    • v.58 no.4
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    • pp.352-358
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    • 2005
  • Microsatellites are short tandem repeated nucleotide sequences that are present throughout the human genome. Variations in the repeat number or a loss of heterozygosity around the microsatellites have been termed a microsatellite alteration (MA). A MA reflects the genetic instability caused by an impairment in the DNA mismatch repair system and is suggested to be a novel tumorigenic mechanism. A number of studies have reported that MA in the DNA extracted from the plasma occurs at varying frequencies among patients with a non-small cell lung carcinoma (NSCLC). The genomic DNA from 9 subjects with a non-small cell lung cancer (squamous cell cancer 6, adenocarcinoma 2, non-small cell lung cancer1) and 9 age matched non-cancer control subjects (AMC: tuberculosis 3, other inflammatory lung disease 6) and 12 normal control subjects (NC) were extracted from the peripheral blood leukocytes and plasma. Three microsatellite loci were amplified with the primers targeting the Gene Bank sequence D21S1245, D3S1300, and D3S1234. MA in the form of an allelic loss or a band shift was examined with 6% polyacrylamide gel electrophoresis and silver staining. None (0/12) of the NC subjects less than 40 years of age showed a MA in any of the three markers, while 88.9%(8/9) of the AMC above 40 showed a MA in at least one of the three markers (p<0.05). Sixty percent(6/10) of the control subjects with a smoking history showed a MA in one of the three markers, while 9.1%(1/11) of the control subjects without smoking history showed a MA (p<0.05). However, not only did 66.7%(6/9) of lung cancer patients show a MA in at least one of the three markers but so did 88.9%(8/21) of the AMC patients (p>0.05). In conclusion, a MA in the D21S1245, D3S1300, and D3S1234 loci using DNA extracted from the plasma was detected in 66.7% of lung cancer while no MA was found in the young non-smoking control subjects. However, many of the non-cancer control subjects (aged smokers) also showed a MA, which compromised the specificity of the MA analysis as a screening test. Therefore, a further study with a larger sample size will be needed.