• Title/Summary/Keyword: DNA profile

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Comparative Analysis of Local Green Tea in Korea by STS-RFLP (STS-RFLP법을 이용한 국내지역 재배녹차의 비교분석)

  • Cho, Kiu-Hyung;Jo, Aruna;Tsuge, Tomohiko;Kim, Jong-Cheol;Kim, Ru-Mi;Yoon, Ho-Sung;Kim, Gyung-Tae
    • Journal of Life Science
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    • v.20 no.9
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    • pp.1415-1419
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    • 2010
  • Consumption of green tea has increased along with increasing concern regarding healthier lifestyles, and many brands of green tea are sold with a label indicating the region of Korea in which the tea was produced. However, there is little information on identifying the difference between the green tea cultivars according to the region they were grown. Here, 9 green tea cultivars collected from Hadong region, Bosung region, China and Japan were subjected to the STS-RFLP analysis. Using the coding and noncoding DNA regions of genes related to the phenylpropanoid pathway, such as phenylalanine ammonia-lyase, chalcone synthase and dihydroflavonol 4-reductase, we have identified the differences between green tea cultivars according to the region they were grown in. In this study, we showed a STS-RFLP method of green tea analysis which easily distinguished different kinds of tea using the primers as described. In addition, we identified that the green tea cultivars from Hadong and Bosung displayed a different profile when PAL intron was digested with Dde I, suggesting that a rapid authentication system for green tea cultivars grown in different regions in Korea is available.

Expressed sequence tag analysis of Meretrix lusoria (Veneridae) in Korea (한국산 백합 (Meretrix lusoria) 의 전사체 분석)

  • Kang, Jung-Ha;Jeong, Ji Eun;Kim, Bong Seok;An, Chel-Min;Kang, Hyun-Sook;Kang, Se-Won;Hwang, Hee Ju;Han, Yeon Soo;Chae, Sung-Hwa;Ko, Hyun-Sook;Lee, Jun-Sang;Lee, Yong Seok
    • The Korean Journal of Malacology
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    • v.28 no.4
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    • pp.377-384
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    • 2012
  • The importance of biological resources has been gradually increasing, and mollusks have been utilized as main fishery resources in terrestrial ecosystems. But little is known about genomic and transcriptional analysis in mollusks. This is the first report on the transcriptomic profile of Meretrix lusoria. In this study, we constructed cDNA library and determined 542 of distinct EST sequences composed of 284 singletons and 95 contigs. At first, we identified 180 of EST sequences that have significant hits on protein sequences of the exclusive Mollusks database through BLASTX program and 343 of EST sequences that have significant hits on NCBI NR database. We also found that 211 of putative sequences through local BLAST (blastx, E < e-10) search against KOG database were classified into 16 functional categories. Some kinds of immune response related genes encoding allograft inflammatory factor 1 (AIF-1), B-cell translocation gene 1 (BTG1), C-type lectin A, thioester-containing protein and 26S proteasome regulatory complex were identified. To determine phylogenetic relationship, we identified partial sequences of four genes (COX1, COX2, 12S rRNA and NADH dehydrogenase) that significantly matched with the mitochondrial genomes of 3 species-Ml (Meretrix lusoria), Mp (Meretrix petechialis) and Mm (Meretrix meretrix). As a result, we found that there was a little bit of a difference between sequences of Korean isolates and other known isolates. This study will be useful to develop breeding technology and might also be helpful to establish a classification system.

Analysis of Genes Expressed in Mouse Ovaries of Early Developmental Stages (초기발달 단계의 생쥐 난소에서 발현하는 유전자에 관한 연구)

  • Jeon Eun-Hyun;Yoon Se-Jin;Cha Kwang-Yul;Kim Nam-Hyung;Lee Kyung-Ah
    • Development and Reproduction
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    • v.7 no.2
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    • pp.127-136
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    • 2003
  • The present study was conducted to investigate gene expression profile of mouse ovaries during the primordial-primary follicle transition. We isolated total RNA from mouse ovaries at day1(contains only primordial follicles) and day5(contains both primordial and primary follicles) and synthesized cDNA using annealing control primers(ACP, Seegene, Inc., Seoul, Korea). Using 80 different ACPs for PCR, we cloned, sequenced, and analyzed identities of 41 differentially expressed genes(DEGs). According to BLAST analysis, sequences of 33 clones significantly matched database entries, 4 clones were novel, and 4 clones were ESTs. We selected 8 DEGs with interesting functions, Anx11 and Pepp2-Pending highly expressed in day1 ovary, while Apg3/Autlp-like, BPOZ, Ches1, Kcmf1, NHE3, Nid2, Ninj1, SENP3, Suil-rsl, and TIAP/m-survivin highly expressed in days ovary, and confirmed their different expression between day1 ovaries and days ovaries using semi-quantitative RT-PCR. There was no false positive result. Using in situ hybridization, we found that almost all of genes studied were expressed in the oocyte from primordial follicle stage but expression decreased from primary follicle stage. Meanwhile their expression was increased in cuboidal granulosa cells. Different expression of BPOZ and TIAP/m-survivin between primordial and primary follicles was confirmed by using laser capture microdissection followed by real-time PCR BPOZ and TIAP/m-survivin expressed 4.5 and 3.4 fold higher in primary than primordial follicles, respectively. List of genes obtained from the present study will provide insights for the study of mechanism regulating primordial-primary follicle transition.

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Matrine Reduces Proliferation of Human Lung Cancer Cells by Inducing Apoptosis and Changing miRNA Expression Profiles

  • Liu, Yong-Qi;Li, Yi;Qin, Jie;Wang, Qian;She, Ya-Li;Luo, Ya-Li;He, Jian-Xin;Li, Jing-Ya;Xie, Xiao-Dong
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.5
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    • pp.2169-2177
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    • 2014
  • Matrine, a main active component extracted from dry roots of Sophora flavecens, has been reported to exert antitumor effects on A549 human non-small lung cancer cells, but its mechanisms of action remain unclear. To determine effects of matrine on proliferation of A549 cells and assess possible mechanisms, MTT assays were employed to detect cytotoxicity, along with o flow cytometric analysis of DNA content of nuclei of cells following staining with propidium iodide to analyze cell cycle distribution. Western blotting was performed to determined expression levels of Bax, Bcl-2, VEGF and HDAC1, while a microarray was used to assessed changes of miRNA profiles. In the MTT assay, matrine suppressed growth of human lung cancer cell A549 in a dose- and timedependent manner at doses of 0.25-2.5 mg/ml for 24h, 48h or 72h. Matrine induced cell cycle arrest in G0/G1 phase and decreased the G2/M phase, while down-regulating the expression of Bcl2 protein, leading to a reduction in the Bcl-2/Bax ratio. In addition, matrine down regulated the expression level of VEGF and HDAC1 of A549 cells. Microarray analysis demonstrated that matrine altered the expression level of miRNAs compared with untreated control A549 cells. In conclusion, matrine could inhibit proliferation of A549 cells, providing useful information for understanding anticancer mechanisms.

Characterization of a new cultivar of Auricularia auricula-judae 'Yong-A' (목이 신품종 '용아'의 특성)

  • Kim, Kil-Ja;Kim, Dami;Lee, Sook-Jae;An, Ho-Sub;Kim, Dong-Kwan;Kwon, Oh-Do
    • Journal of Mushroom
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    • v.16 no.3
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    • pp.198-202
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    • 2018
  • 'Yong-A' was bred by Jeollanamdo Agricultural Research and Extension Services in 2015. It was primarily selected through monospore crossing between JNM21008 and JNM21013 in 2009. The strain is named as JNM-Mi-194 and 'Yong-A', showing major characteristics with good production yield. The cultivation characteristics, yield potential, and fruiting body characteristics of 'Yong-A' are as follows; The wrinkle of the fruiting body was of branching type its shape was wave type. MCM, YM, Malt, and PDA media were suitable for growth of this cultivar. The number of effective stipes was 13 ea/0.9 kg. The minor axis of pileus was 5 cm and the major axis was 9 cm. The yield was 291 g per plastic bag (0.9 kg). Yong-A required 60 days for mycelial running at $20^{\circ}C$. The growth and primordial period required 24 days, which was shorter than that of JNM-Mi-21002 (the conventional cultivar). Somatic incompatibility was observed between parental lines and Yong-A. Analysis of genetic diversity in the new variety 'Yong-A' showed a different profile compared to that of the parent strain when Random Amplified Polymorphic DNA primers were used.

Genetic characterization of Shigella flexneri isolated from the diarrheic patients in Seoul region (서울지역 설사환자로 부터 분리된 Shigella flexneri의 성상과 유전적 특성)

  • Seung, Hyun-Jung;Kim, Moo-Sang;Oh, Young-Hee;Choi, Byung-Hyun;Chae, Hee-Sun;Chu, Jiaqi;Jun, Moo-Hyung
    • Korean Journal of Veterinary Research
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    • v.46 no.4
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    • pp.337-345
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    • 2006
  • The shigellae are common etiological agents of bacillary dysentery in humans and primates. During four years from 2002 to 2005, 22 strains of Shigella spp. were isolated from the diarrheic patients in Seoul region. All of them were identified as S. flexneri by biochemical tests and serotyping. The prevalence of serotypes were variable by year, but the major serotypes were 2a and 3a. In an antimicrobial susceptibility test, all of the isolates were resistant to streptomycin and tetracycline, and susceptible to amikacin, kanamycin, cefoxitin, and gentamicin. All of the isolates showed the multi-resistant patterns over 3 drugs. By analysis of the plasmid profile the isolates were classified into 7 groups (P1~P7). Serotypes 2a and 2b were distributed to P1, P2, P3, and P4. Serotype 3a was differentiated to P5 and serotype 3b, to P6 and serotype 4a, to P7. PCR results showed that all isolates were positive for two virulence genes, ipaH and ial, but none of the strains had stx gene. The set1A and set1B genes were detected from 12 isolates (54.5%) that belonged to serotype 2a and 2b. The sen gene was detected from 19 isolates (86.4%). The 22 isolates showed 12 to 17 DNA fragments in the sizes ranging from 20.5 kb to 1135 kb, resulting in 13 patterns by the PFGE with Not I digestion. The PFGE patterns of the isolates showed the close relation with the serotypes, but no relations with year of isolation and antimicrobial resistance.

Comparison of Harboring the Resistance Gene and Disc Diffusion Susceptibility Test Result in Staphylococcus pseudintermedius from the Bacterial Dermatitis (세균성 피부염 개에서 분리된 Staphylococcus pseudintermedius에서 항생제 감수성 검사와 내성 유전자 획득의 비교)

  • Jang, Hye-Jin;Son, Hyoung-Won;Kang, Hyo-Min;Han, Jae-Ik;Na, Ki-Jeong
    • Journal of Veterinary Clinics
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    • v.32 no.2
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    • pp.158-161
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    • 2015
  • Bacterial dermatitis is common disease that is necessary to treat with antibiotics. In recent, antibiotic-resistant bacteria is being increased in worldwide. The purpose of the present study was to evaluate the prevalence of resistant genes in Staphylococcus (S.) pseudintermedius isolated from dogs, and to compare the resistant gene profile with the result of antibiotic disc diffusion test. A total of seven S. pseudintermedius was included in the study. Bacterial identification was performed by 16S ribosomal RNA gene sequence analysis. S. pseudintermedius isolates had more than one antibiotic resistant gene (mecA, blaZ and aac(6')/aph(2"). While all isolates were PCR positive to blaZ gene, only two isolates were resistant to amoxicillin/clavulanate. Among five isolates harboring gentamicin resistance, one isolate was negative to aac(6')/aph(2")-targeted PCR. Taken together, the results suggest that resistant gene-targeted PCR and disc diffusion test are complementary to detect antibiotic resistance.

Protective Effects of Samul-tang on Oxidative Stress induced Death of H9c2 Cardioblast Cells (배양심근세포의 산화적 손상에 대한 사물탕의 방어효과)

  • Cho Kwon-Il;Jung Seung-Won;Jang Jae-Ho;Lee Dae-Yong;Park Sae-Wook;Lee In;Sin Sun-Ho;Moon Byung-Soon
    • The Journal of Korean Medicine
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    • v.26 no.1 s.61
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    • pp.174-186
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    • 2005
  • Objectives : The water extract of Samul-tang (SMT) has traditionally been used for treatment of ischemic heart and brain damage in oriental medicine. However, little is known about the mechanism by which the water extract of SMT rescues cells from these damages. Methods: This study was designed to investigate the protective mechanisms of SMT on oxidative stress-induced toxicity in H9c2 cardiomyoblast cells. Treatment with $H_2O_2$ markedly induced death of H9c2 cardiomyoblast cells in a dose-dependent manner. Results: The characteristics of H20z-induced death of H9c2 showed apparent apoptotic features such as DNA fragmentation and morphological change. However, SMT significantly reduced both H202-induced cell death and morphological change. The decrease of Bc-2 expression by High were inhibited by SMT. In addition, the increase of Bax expression was also inhibited by SMT. The cotreatment of SMT and $H_2O_2$ in H9c2 cells also induced the phosphorylation of ERK in a time-dependent manner. Moreover, PD98059, a specific inhibitor of ERK1/2 attenuated the protective effects of SMT on $H_2O_2-induced$ toxicity in H9c2 cardiomyoblast cells. These results suggest that both ERK1/2 signaling pathways play important roles in the protective effects of SMT on $H_2O_2-induced$ apoptotic death of H9c2 cells. Also, the expression profile of proteins in $H_2O_2$ cardiomyoblast cells were screened by using two-dimensional (2-D) gel electrophoresis. Among 300 spots resolved in 2-D gels, the comparison of control versus apoptosis cells revealed that signal intensity of 17 spots increased and 11 spots decreased. Conclusions: Taken together, this study suggests that the protectiw effects of the water extract of SMT against oxidative damages may be mediated by the modulation of Bc1-2 and Bax expression via the regulation of the ERK signaling pathway.

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Association between Periodontitis and Coronary heart disease in Korea : Inflammatory markers and IL-1 gene polymorphism (한국인에서 치주질환과 관상동맥질환의 관련성에 대한 염증표지자와 IL-1 유전자 다변성의 영향)

  • Jeong, Ha-Na;Chung, Hyun-Ju;Kim, Ok-Su;Kim, Young-Joon;Kim, Ju-Han;Koh, Jung-Tae
    • Journal of Periodontal and Implant Science
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    • v.34 no.3
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    • pp.607-622
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    • 2004
  • Recently epidemiologic studies have indicated that the patients with periodontitis may have increased risk of ischemic cardiovascular events, and have suggested the important roles of blood cytokines and acute reactant proteins in the systemic infection and inflammatory response. Periodontitis and coronary heart disease (CHD) may share the common risk factors and the genetic mechanism associated with interleukin(IL)-1A, B and RA genotype may be involved in the production of IL-1. This study was aimed to investigate the relationship between angiographically defined CHD and periodontitis as chronic Gram-negative bacterial infection and to determine whether the IL-1 gene polymorphism is associated in both diseases. Patients under the age of 60 who had undergone diagnostic coronary angiography were enrolled in this study. Subjects were classified as positive CHD (+CHD, n=37) with coronary artery stenosis more than 50% in at least one of major epicardial arteries, and negative CHD (-CHD, n=30) without significant stenosis. After recording the number of missing teeth, periodontal disease severity was measured by means of plaque index (PI), gingival index (GI), bleeding on probing (BOP), probing depth (PD), clinical attachment level (CAL), and radiographic bone loss around all remaining teeth. Gingival crevicular fluid (GCF) was collected from the 4 deepest periodontal pockets and assessed for cytokine ($IL-1{\beta}$, IL-6, IL-1ra, tumor necrosis $factor-{\alpha}$, and prostaglandin $E_2$). Additionally, blood CHD markers, lipid profile, and blood cytokines were analyzed. IL-1 gene cluster genotyping was performed by polymerase chain reaction and enzyme restriction using genomic DNA from buccal swab, and allele 2 frequencies of IL-1A(+4845), IL-1B(+3954), IL-B(-511), and IL-1RA(intron 2) were compared between groups. Even though there was no significant difference in the periodontal parameters between 2 groups, GCF level of $PGE_2$ was significantly higher in the +CHD group(p<0.05). Correlation analysis showed the positive relationship among PD, CAL and coronary artery stenosis(%) and blood $PGE_2$. There was also significant positive relationship between the periodontal parameters (PI, PD, CAL) and the blood CHD markers (leukocyte count, C-reactive protein, and lactic dehyrogenase). IL-1 gene genotyping showed that IL-1A(+3954) allele 2 frequency was significantly higher in the +CHD group compared with the -CHD group (15% vs. 3.3%, OR 5.118,p=0.043). These results suggested that periodontal inflammation is related to systemic blood cytokine and CHD markers, and contributes to cardiovascular disease via systemic inflammatory reaction. IL-1 gene polymorphism might have an influence on periodontal and coronary heart diseases in Korean patients.

Gene Expression Profile of Lung Cancer Cells Following Photodynamic Therapy (폐암 세포주에서 광역학 치료에 의한 유전자 발현 분석)

  • Sung, Ji Hyun;Lee, Mi-Eun;Han, Seon-Sook;Lee, Seung-Joon;Ha, Kwon-Soo;Kim, Woo Jin
    • Tuberculosis and Respiratory Diseases
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    • v.63 no.1
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    • pp.52-58
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    • 2007
  • Background: Photodynamic therapy is a viable option for lung cancer treatment, and many studies have shown that it is capable of inducing cell death in lung cancer cells. However, the precise mechanism of this cell death has not been fully elucidated. To investigate the early changes in cancer cell transcription, we treated A549 cells with the photosensitizer DH-I-180-3 and then we illuminated the cells. Methods: We investigated the gene expression profiles of the the A549 lung cancer cell line, using a DEG kit, following photodynamic therapy and we evaluated the cell viability by performing flow cytometry. We identified the genes that were significantly changed following photodynamic therapy by performing DNA sequencing. Results: The FACS data showed that the cell death of the lung cancer cells was mainly caused by necrosis. We found nine genes that were significantly changed and we identified eight of these genes. We evaluated the expression of two genes, 3-phosphoglycerate dehydrogenase and ribosomal protein S29. The expressed level of carbonic anhydrase XII, clusterin, MRP3s1 protein, complement 3, membrane cofactor protein and integrin beta 1 were decreased. Conclusion: Many of the gene products are membrane-associated proteins. The main mechanism of photodynamic therapy with using the photosensitizing agent DH-I-180-3 appears to be necrosis and this may be associated with the altered production of membrane proteins.